/tools/metag_tools/shrimp_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 279 lines · 184 code · 38 blank · 57 comment · 0 complexity · 32a5b3c6112411b2534b8d8e8178df9d MD5 · raw file 

    

  1. <tool id="shrimp_wrapper" name="SHRiMP for Letter-space" version="1.0.0">
    2. 

  2.   <description>reads mapping against reference sequence </description>
    3. 

  3.   <command interpreter="python">
    4. 

  4.     #if     ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip") #shrimp_wrapper.py $input_target $output1 $output2 $input_query
    5. 

  5.     #elif   ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip") #shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size
    6. 

  6.     #elif   ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full") #shrimp_wrapper.py $input_target $output1 $output2 $input_query                                                              $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold 
    7. 

  7.     #elif   ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full") #shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold
    8. 

  8.     #end if#
    9. 

  9.   </command>
    10. 

  10.     <inputs>
    11. 

  11.         <page>
    12. 

  12.         <conditional name="type_of_reads">
    13. 

  13.             <param name="single_or_paired" type="select" label="Single- or Paired-ends">
    14. 

  14.                 <option value="single">Single-end</option>
    15. 

  15.                 <option value="paired">Paired-end</option>
    16. 

  16.             </param>
    17. 

  17.             <when value="single">
    18. 

  18.                 <param name="input_query" type="data" format="fastqsolexa" label="Align sequencing reads" help="No dataset? Read tip below"/>
    19. 

  19.             </when>
    20. 

  20.             <when value="paired">
    21. 

  21.                 <param name="insertion_size" type="integer" size="5" value="600" label="Insertion length between two ends" help="bp" />
    22. 

  22.                 <param name="input1" type="data" format="fastqsolexa" label="Align sequencing reads, one end" />
    23. 

  23.                 <param name="input2" type="data" format="fastqsolexa" label="and the other end" />
    24. 

  24.             </when> 
    25. 

  25.         </conditional>
    26. 

  26.         <param name="input_target" type="data" format="fasta" label="against reference" />
    27. 

  27.         <conditional name="param">
    28. 

  28.             <param name="skip_or_full" type="select" label="SHRiMP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
    29. 

  29.                 <option value="skip">Commonly used</option>
    30. 

  30.                 <option value="full">Full Parameter List</option>
    31. 

  31.             </param>
    32. 

  32.             <when value="skip" />
    33. 

  33.             <when value="full">
    34. 

  34.                 <param name="spaced_seed"                   type="text"     size="30"   value="111111011111"    label="Spaced Seed" />
    35. 

  35.                 <param name="seed_matches_per_window"       type="integer"  size="5"    value="2"               label="Seed Matches per Window" />
    36. 

  36.                 <param name="seed_hit_taboo_length"         type="integer"  size="5"    value="4"               label="Seed Hit Taboo Length" />
    37. 

  37.                 <param name="seed_generation_taboo_length"  type="integer"  size="5"    value="0"               label="Seed Generation Taboo Length" />
    38. 

  38.                 <param name="seed_window_length"            type="float"    size="10"   value="115.0"           label="Seed Window Length"          help="in percentage"/>
    39. 

  39.                 <param name="max_hits_per_read"             type="integer"  size="10"   value="100"             label="Maximum Hits per Read" />
    40. 

  40.                 <param name="max_read_length"               type="integer"  size="10"   value="1000"            label="Maximum Read Length" />
    41. 

  41.                 <param name="kmer"                          type="integer"  size="10"   value="-1"              label="Kmer Std. Deviation Limit"   help="-1 as None"/>
    42. 

  42.                 <param name="sw_match_value"                type="integer"  size="10"   value="100"             label="S-W Match Value" />
    43. 

  43.                 <param name="sw_mismatch_value"             type="integer"  size="10"   value="-150"            label="S-W Mismatch Value" />
    44. 

  44.                 <param name="sw_gap_open_ref"               type="integer"  size="10"   value="-400"            label="S-W Gap Open Penalty (Reference)" />
    45. 

  45.                 <param name="sw_gap_open_query"             type="integer"  size="10"   value="-400"            label="S-W Gap Open Penalty (Query)" />
    46. 

  46.                 <param name="sw_gap_ext_ref"                type="integer"  size="10"   value="-70"             label="S-W Gap Extend Penalty (Reference)" />
    47. 

  47.                 <param name="sw_gap_ext_query"              type="integer"  size="10"   value="-70"             label="S-W Gap Extend Penalty (Query)" />
    48. 

  48.                 <param name="sw_hit_threshold"              type="float"    size="10"   value="68.0"            label="S-W Hit Threshold"           help="in percentage"/>
    49. 

  49.             </when>
    50. 

  50.         </conditional>
    51. 

  51.         </page>
    52. 

  52.     </inputs>
    53. 

  53.     <outputs>
    54. 

  54.         <data name="output1" format="tabular"/>
    55. 

  55.         <data name="output2" format="tabular"/>
    56. 

  56.     </outputs>
    57. 

  57.     <requirements>
    58. 

  58.       <requirement type="binary">rmapper-ls</requirement>
    59. 

  59.     </requirements>
    60. 

  60.     <tests>
    61. 

  61.         <test>
    62. 

  62.             <param name="single_or_paired" value="single" />
    63. 

  63.             <param name="skip_or_full" value="skip" />
    64. 

  64.             <param name="input_target" value="shrimp_phix_anc.fa" ftype="fasta" />
    65. 

  65.             <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/>
    66. 

  66.             <output name="output1" file="shrimp_wrapper_test1.out1" />
    67. 

  67.         </test>
    68. 

  68.         <!--  
    69. 

  69.         <test>
    70. 

  70.             <param name="single_or_paired" value="paired" />
    71. 

  71.             <param name="skip_or_full" value="skip" />
    72. 

  72.             <param name="input_target" value="shrimp_eca_chrMT.fa" ftype="fasta" />
    73. 

  73.             <param name="input1" value="shrimp_wrapper_test2_end1.fastq" ftype="fastqsolexa" />
    74. 

  74.             <param name="input2" value="shrimp_wrapper_test2_end2.fastq" ftype="fastqsolexa" />
    75. 

  75.             <param name="insertion_size" value="600" />
    76. 

  76.             <output name="output1" file="shrimp_wrapper_test2.out1" />
    77. 

  77.         </test>
    78. 

  78.         <test>
    79. 

  79.             <param name="single_or_paired" value="single" />
    80. 

  80.             <param name="skip_or_full" value="full" />
    81. 

  81.             <param name="input_target" value="shrimp_phix_anc.fa" ftype="fasta" />
    82. 

  82.             <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/>
    83. 

  83.             <param name="spaced_seed" value="111111011111" />
    84. 

  84.             <param name="seed_matches_per_window" value="2" />
    85. 

  85.             <param name="seed_hit_taboo_length" value="4" />
    86. 

  86.             <param name="seed_generation_taboo_length" value="0" />
    87. 

  87.             <param name="seed_window_length" value="115.0" />
    88. 

  88.             <param name="max_hits_per_read" value="100" />
    89. 

  89.             <param name="max_read_length" value="1000" />
    90. 

  90.             <param name="kmer" value="-1" />
    91. 

  91.             <param name="sw_match_value" value="100" />
    92. 

  92.             <param name="sw_mismatch_value" value="-150" />
    93. 

  93.             <param name="sw_gap_open_ref" value="-400" />
    94. 

  94.             <param name="sw_gap_open_query" value="-400" />
    95. 

  95.             <param name="sw_gap_ext_ref" value="-70" />
    96. 

  96.             <param name="sw_gap_ext_query" value="-70" />
    97. 

  97.             <param name="sw_hit_threshold" value="68.0" />
    98. 

  98.             <output name="output1" file="shrimp_wrapper_test1.out1" />
    99. 

  99.         </test> 
    100. 

  100.         <test>
    101. 

  101.             <param name="single_or_paired" value="paired" />
    102. 

  102.             <param name="skip_or_full" value="full" />
    103. 

  103.             <param name="input_target" value="shrimp_eca_chrMT.fa" ftype="fasta" />
    104. 

  104.             <param name="spaced_seed" value="111111011111" />
    105. 

  105.             <param name="seed_matches_per_window" value="2" />
    106. 

  106.             <param name="seed_hit_taboo_length" value="4" />
    107. 

  107.             <param name="seed_generation_taboo_length" value="0" />
    108. 

  108.             <param name="seed_window_length" value="115.0" />
    109. 

  109.             <param name="max_hits_per_read" value="100" />
    110. 

  110.             <param name="max_read_length" value="1000" />
    111. 

  111.             <param name="kmer" value="-1" />
    112. 

  112.             <param name="sw_match_value" value="100" />
    113. 

  113.             <param name="sw_mismatch_value" value="-150" />
    114. 

  114.             <param name="sw_gap_open_ref" value="-400" />
    115. 

  115.             <param name="sw_gap_open_query" value="-400" />
    116. 

  116.             <param name="sw_gap_ext_ref" value="-70" />
    117. 

  117.             <param name="sw_gap_ext_query" value="-70" />
    118. 

  118.             <param name="sw_hit_threshold" value="68.0" />
    119. 

  119.             <param name="input1" value="shrimp_wrapper_test2_end1.fastq" ftype="fastqsolexa"/>
    120. 

  120.             <param name="input2" value="shrimp_wrapper_test2_end2.fastq" ftype="fastqsolexa"/>
    121. 

  121.             <param name="insertion_size" value="600" />
    122. 

  122.             <output name="output1" file="shrimp_wrapper_test2.out1" />
    123. 

  123.         </test>
    124. 

  124.         -->
    125. 

  125.     </tests>
    126. 

  126. <help>
    127. 

  127. 

  128. .. class:: warningmark
    129. 

  129. 

  130. IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64. Click pencil icon next to your dataset to set datatype to *fastqsolexa*.
    131. 

  131. 

  132. 

  133. -----
    134. 

  134.     
    135. 

  135. **What it does**
    136. 

  136.  
    137. 

  137. SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome. 
    138. 

  138. 

  139. This wrapper post-processes the default SHRiMP/rmapper-ls output and generates a table with all information from reads and reference for the mapping. The tool takes single- or paired-end reads. For single-end reads, only uniquely mapped alignment is considered. In paired-end reads, only pairs that meet the following criteria will be used to generate the table: 1). the ends fall within the insertion size; 2). the ends are mapped at the opposite directions. If there are still multiple mappings after applying the criteria, this paired-end read will be discarded. 
    140. 

  140.   
    141. 

  141. 

  142. -----
    143. 

  143. 

  144. **Input formats**
    145. 

  145. 

  146. A multiple-fastq file, for example::
    147. 

  147. 

  148.     @seq1
    149. 

  149.     TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT
    150. 

  150.     +seq1
    151. 

  151.     hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
    152. 

  152. 

  153. 

  154. -----
    155. 

  155. 

  156. **Outputs**
    157. 

  157. 

  158. The tool gives two outputs.
    159. 

  159. 

  160. **Table output**
    161. 

  161. 

  162. Table output contains 8 columns::
    163. 

  163. 

  164.      1     2        3       4     5     6     7     8 
    165. 

  165.   ----------------------------------------------------
    166. 

  166.   chrM   14711     seq1     0     T     A    40     1 
    167. 

  167.   chrM   14712     seq1     1     T     T    40     1 
    168. 

  168. 

  169. where::
    170. 

  170.     
    171. 

  171.   1. (chrM)   - Reference sequence id
    172. 

  172.   2. (14711)  - Position of the mapping in the reference
    173. 

  173.   3. (seq1)   - Read id
    174. 

  174.   4. (0)      - Position of the mapping in the read
    175. 

  175.   5. (T)      - Nucleotide in the reference
    176. 

  176.   6. (A)      - Nucleotide in the read
    177. 

  177.   7. (40)     - Quality score for the nucleotide in the position of the read
    178. 

  178.   8. (1)      - The number of times this position is covered by reads
    179. 

  179. 

  180.      
    181. 

  181. **SHRiMP output**
    182. 

  182. 

  183. This is the default output from SHRiMP/rmapper-ls::
    184. 

  184.  
    185. 

  185.      1     2     3       4      5      6     7     8      9      10
    186. 

  186.   -------------------------------------------------------------------
    187. 

  187.    seq1  chrM    +     3644    3679    1    36     36    3600    36  
    188. 

  188. 

  189. where::
    190. 

  190. 

  191.   1. (seq1)   - Read id 
    192. 

  192.   2. (chrM)   - Reference sequence id
    193. 

  193.   3. (+)      - Strand of the read
    194. 

  194.   4. (3466)   - Start position of the alignment in the reference
    195. 

  195.   5. (3679)   - End position of the alignment in the reference
    196. 

  196.   6. (1)      - Start position of the alignment in the read
    197. 

  197.   7. (36)     - End position of the alignment in the read
    198. 

  198.   8. (36)     - Length of the read
    199. 

  199.   9. (3600)   - Score 
    200. 

  200.  10. (36)     - Edit string
    201. 

  201. 

  202.  
    203. 

  203. -----
    204. 

  204. 

  205. **SHRiMP parameter list**
    206. 

  206. 

  207. The commonly used parameters with default value setting::
    208. 

  208. 

  209.     -s    Spaced Seed                             (default: 111111011111)
    210. 

  210.           The spaced seed is a single contiguous string of 0's and 1's. 
    211. 

  211.           0's represent wildcards, or positions which will always be 
    212. 

  212.           considered as matching, whereas 1's dictate positions that 
    213. 

  213.           must match. A string of all 1's will result in a simple kmer scan.
    214. 

  214.     -n    Seed Matches per Window                 (default: 2)
    215. 

  215.           The number of seed matches per window dictates how many seeds 
    216. 

  216.           must match within some window length of the genome before that 
    217. 

  217.           region is considered for Smith-Waterman alignment. A lower 
    218. 

  218.           value will increase sensitivity while drastically increasing 
    219. 

  219.           running time. Higher values will have the opposite effect.
    220. 

  220.     -t    Seed Hit Taboo Length                   (default: 4)
    221. 

  221.           The seed taboo length specifies how many target genome bases 
    222. 

  222.           or colors must exist prior to a previous seed match in order 
    223. 

  223.           to count another seed match as a hit.
    224. 

  224.     -9    Seed Generation Taboo Length            (default: 0)
    225. 

  225.           
    226. 

  226.     -w    Seed Window Length                      (default: 115.00%)
    227. 

  227.           This parameter specifies the genomic span in bases (or colours) 
    228. 

  228.           in which *seed_matches_per_window* must exist before the read 
    229. 

  229.           is given consideration by the Simth-Waterman alignment machinery.
    230. 

  230.     -o    Maximum Hits per Read                   (default: 100)
    231. 

  231.           This parameter specifies how many hits to remember for each read. 
    232. 

  232.           If more hits are encountered, ones with lower scores are dropped 
    233. 

  233.           to make room.
    234. 

  234.     -r    Maximum Read Length                     (default: 1000)
    235. 

  235.           This parameter specifies the maximum length of reads that will 
    236. 

  236.           be encountered in the dataset. If larger reads than the default 
    237. 

  237.           are used, an appropriate value must be passed to *rmapper*.
    238. 

  238.     -d    Kmer Std. Deviation Limit               (default: -1 [None])
    239. 

  239.           This option permits pruning read kmers, which occur with 
    240. 

  240.           frequencies greater than *kmer_std_dev_limit* standard 
    241. 

  241.           deviations above the average. This can shorten running 
    242. 

  242.           time at the cost of some sensitivity. 
    243. 

  243.           *Note*: A negative value disables this option.            
    244. 

  244.     -m    S-W Match Value                         (default: 100)
    245. 

  245.           The value applied to matches during the Smith-Waterman score calculation.
    246. 

  246.     -i    S-W Mismatch Value                      (default: -150)
    247. 

  247.           The value applied to mismatches during the Smith-Waterman 
    248. 

  248.           score calculation.
    249. 

  249.     -g    S-W Gap Open Penalty (Reference)        (default: -400)
    250. 

  250.           The value applied to gap opens along the reference sequence 
    251. 

  251.           during the Smith-Waterman score calculation.
    252. 

  252.           *Note*: Note that for backward compatibility, if -g is set 
    253. 

  253.           and -q is not set, the gap open penalty for the query will 
    254. 

  254.           be set to the same value as specified for the reference.
    255. 

  255.     -q    S-W Gap Open Penalty (Query)            (default: -400)
    256. 

  256.           The value applied to gap opens along the query sequence during 
    257. 

  257.           the Smith-Waterman score calculation.        
    258. 

  258.     -e    S-W Gap Extend Penalty (Reference)      (default: -70)
    259. 

  259.           The value applied to gap extends during the Smith-Waterman score calculation.
    260. 

  260.           *Note*: Note that for backward compatibility, if -e is set 
    261. 

  261.           and -f is not set, the gap exten penalty for the query will 
    262. 

  262.           be set to the same value as specified for the reference. 
    263. 

  263.     -f    S-W Gap Extend Penalty (Query)          (default: -70)
    264. 

  264.           The value applied to gap extends during the Smith-Waterman score calculation.
    265. 

  265.     -h    S-W Hit Threshold                       (default: 68.00%)
    266. 

  266.           In letter-space, this parameter determines the threshold 
    267. 

  267.           score for both vectored and full Smith-Waterman alignments. 
    268. 

  268.           Any values less than this quantity will be thrown away.
    269. 

  269.           *Note* This option differs slightly in meaning between letter-space and color-space.
    270. 

  270. 

  271. 

  272. -----
    273. 

  273. 

  274. **Reference**
    275. 

  275.  
    276. 

  276.  **SHRiMP**: Stephen M. Rumble, Michael Brudno, Phil Lacroute, Vladimir Yanovsky, Marc Fiume, Adrian Dalca. shrimp at cs dot toronto dot edu. 
    277. 

  277. 

  278. </help>
    279. 

  279. </tool>
    280.