/tools/metag_tools/shrimp_color_wrapper.xml
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1<tool id="shrimp_color_wrapper" name="SHRiMP for Color-space" version="1.0.0"> 2 <description>reads mapping against reference sequence </description> 3 <command interpreter="python"> 4 #if $param.skip_or_full=="skip" #shrimp_color_wrapper.py $input_target $input_query $output1 5 #else #shrimp_color_wrapper.py $input_target $input_query $output1 $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_crossover_penalty $param.sw_full_hit_threshold $param.sw_vector_hit_threshold 6 #end if# 7 </command> 8 <inputs> 9 <page> 10 <param name="input_query" type="data" format="csfasta" label="Align sequencing reads" help="No dataset? Read tip below"/> 11 <param name="input_target" type="data" format="fasta" label="against reference" /> 12 <conditional name="param"> 13 <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"> 14 <option value="skip">Commonly used</option> 15 <option value="full">Full Parameter List</option> 16 </param> 17 <when value="skip" /> 18 <when value="full"> 19 <param name="spaced_seed" type="text" size="30" value="1111001111" label="Spaced Seed" /> 20 <param name="seed_matches_per_window" type="integer" size="5" value="2" label="Seed Matches per Window" /> 21 <param name="seed_hit_taboo_length" type="integer" size="5" value="4" label="Seed Hit Taboo Length" /> 22 <param name="seed_generation_taboo_length" type="integer" size="5" value="0" label="Seed Generation Taboo Length" /> 23 <param name="seed_window_length" type="float" size="10" value="115.0" label="Seed Window Length" help="in percentage"/> 24 <param name="max_hits_per_read" type="integer" size="10" value="100" label="Maximum Hits per Read" /> 25 <param name="max_read_length" type="integer" size="10" value="1000" label="Maximum Read Length" /> 26 <param name="kmer" type="integer" size="10" value="-1" label="Kmer Std. Deviation Limit" help="-1 as None"/> 27 <param name="sw_match_value" type="integer" size="10" value="100" label="S-W Match Value" /> 28 <param name="sw_mismatch_value" type="integer" size="10" value="-150" label="S-W Mismatch Value" /> 29 <param name="sw_gap_open_ref" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Reference)" /> 30 <param name="sw_gap_open_query" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Query)" /> 31 <param name="sw_gap_ext_ref" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Reference)" /> 32 <param name="sw_gap_ext_query" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Query)" /> 33 <param name="sw_crossover_penalty" type="integer" size="10" value="-140" label="S-W Crossover Penalty" /> 34 <param name="sw_full_hit_threshold" type="float" size="10" value="68.0" label="S-W Full Hit Threshold" help="in percentage"/> 35 <param name="sw_vector_hit_threshold" type="float" size="10" value="60.0" label="S-W Vector Hit Threshold" help="in percentage"/> 36 </when> 37 </conditional> 38 </page> 39 </inputs> 40 <outputs> 41 <data name="output1" format="tabular"/> 42 </outputs> 43 <requirements> 44 <requirement type="binary">rmapper-cs</requirement> 45 </requirements> 46 <tests> 47 <test> 48 <param name="skip_or_full" value="skip" /> 49 <param name="input_target" value="Ssuis.fasta" ftype="fasta" /> 50 <param name="input_query" value="shrimp_cs_test1.csfasta" ftype="csfasta"/> 51 <output name="output1" file="shrimp_cs_test1.out" /> 52 </test> 53 </tests> 54<help> 55 56.. class:: warningmark 57 58To use this tool your dataset needs to be in the *csfasta* (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set the datatype to *csfasta*. 59 60 61----- 62 63**What it does** 64 65SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome. 66 67 68----- 69 70**Input formats** 71 72A multiple color-space file, for example:: 73 74 >2_263_779_F3 75 T132032030200202202003211302222202230022110222 76 77 78----- 79 80**Outputs** 81 82The tool returns the default SHRiMP output:: 83 84 85 1 2 3 4 5 6 7 8 9 10 86 -------------------------------------------------------------------------------------------------------------------- 87 >2_263_779_F3 Streptococcus_suis + 814344 814388 1 45 45 3660 8x19x3x2x6x4x3 88 89where:: 90 91 1. (>2_263_779_F3) - Read id 92 2. (Streptococcus_suis) - Reference sequence id 93 3. (+) - Strand of the read 94 4. (814344) - Start position of the alignment in the reference 95 5. (814388) - End position of the alignment in the reference 96 6. (1) - Start position of the alignment in the read 97 7. (45) - End position of the alignment in the read 98 8. (45) - Length of the read 99 9. (3660) - Score 100 10. (8x19x3x2x6x4x3) - Edit string 101 102 103----- 104 105**SHRiMP parameter list** 106 107The commonly used parameters with default value setting:: 108 109 -s Spaced Seed (default: 111111011111) 110 The spaced seed is a single contiguous string of 0's and 1's. 111 0's represent wildcards, or positions which will always be 112 considered as matching, whereas 1's dictate positions that 113 must match. A string of all 1's will result in a simple kmer scan. 114 -n Seed Matches per Window (default: 2) 115 The number of seed matches per window dictates how many seeds 116 must match within some window length of the genome before that 117 region is considered for Smith-Waterman alignment. A lower 118 value will increase sensitivity while drastically increasing 119 running time. Higher values will have the opposite effect. 120 -t Seed Hit Taboo Length (default: 4) 121 The seed taboo length specifies how many target genome bases 122 or colours must exist prior to a previous seed match in order 123 to count another seed match as a hit. 124 -9 Seed Generation Taboo Length (default: 0) 125 126 -w Seed Window Length (default: 115.00%) 127 This parameter specifies the genomic span in bases (or colours) 128 in which *seed_matches_per_window* must exist before the read 129 is given consideration by the Simth-Waterman alignment machinery. 130 -o Maximum Hits per Read (default: 100) 131 This parameter specifies how many hits to remember for each read. 132 If more hits are encountered, ones with lower scores are dropped 133 to make room. 134 -r Maximum Read Length (default: 1000) 135 This parameter specifies the maximum length of reads that will 136 be encountered in the dataset. If larger reads than the default 137 are used, an appropriate value must be passed to *rmapper*. 138 -d Kmer Std. Deviation Limit (default: -1 [None]) 139 This option permits pruning read kmers, which occur with 140 frequencies greater than *kmer_std_dev_limit* standard 141 deviations above the average. This can shorten running 142 time at the cost of some sensitivity. 143 *Note*: A negative value disables this option. 144 -m S-W Match Value (default: 100) 145 The value applied to matches during the Smith-Waterman score calculation. 146 -i S-W Mismatch Value (default: -150) 147 The value applied to mismatches during the Smith-Waterman 148 score calculation. 149 -g S-W Gap Open Penalty (Reference) (default: -400) 150 The value applied to gap opens along the reference sequence 151 during the Smith-Waterman score calculation. 152 *Note*: Note that for backward compatibility, if -g is set 153 and -q is not set, the gap open penalty for the query will 154 be set to the same value as specified for the reference. 155 -q S-W Gap Open Penalty (Query) (default: -400) 156 The value applied to gap opens along the query sequence during 157 the Smith-Waterman score calculation. 158 -e S-W Gap Extend Penalty (Reference) (default: -70) 159 The value applied to gap extends during the Smith-Waterman score calculation. 160 *Note*: Note that for backward compatibility, if -e is set 161 and -f is not set, the gap exten penalty for the query will 162 be set to the same value as specified for the reference. 163 -f S-W Gap Extend Penalty (Query) (default: -70) 164 The value applied to gap extends during the Smith-Waterman score calculation. 165 -x 166 -h S-W Full Hit Threshold (default: 68.00%) 167 In letter-space, this parameter determines the threshold 168 score for both vectored and full Smith-Waterman alignments. 169 Any values less than this quantity will be thrown away. 170 *Note* This option differs slightly in meaning between letter-space and color-space. 171 -v 172 173 174----- 175 176**Reference** 177 178 **SHRiMP**: Stephen M. Rumble, Michael Brudno, Phil Lacroute, Vladimir Yanovsky, Marc Fiume, Adrian Dalca. shrimp at cs dot toronto dot edu. 179 180</help> 181</tool>