/tools/peak_calling/ccat_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 148 lines · 125 code · 7 blank · 16 comment · 0 complexity · 3f4417401f31adab4d20a53f58de6ce9 MD5 · raw file 

    

  1. <tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
    2. 

  2.   <description>Control-based ChIP-seq Analysis Tool</description>
    3. 

  3.   <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' 
    4. 

  4.   #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
    5. 

  5.   '$input_advanced_config_file' 
    6. 

  6.   #else:
    7. 

  7.   '${ options_type.input_config_file.fields.path }'
    8. 

  8.   #end if
    9. 

  9.   'CCAT in Galaxy' 
    10. 

  10.   '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command>
    11. 

  11.   <requirements>
    12. 

  12.     <requirement type="binary" version="3.0">CCAT</requirement>
    13. 

  13.   </requirements>
    14. 

  14.   <inputs>
    15. 

  15.     <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" >
    16. 

  16.       <validator type="unspecified_build" />
    17. 

  17.     </param>
    18. 

  18.     <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >
    19. 

  19.       <validator type="unspecified_build" />
    20. 

  20.     </param>
    21. 

  21.     <conditional name="options_type">
    22. 

  22.       <param name="options_type_selector" type="select" label="Advanced Options">
    23. 

  23.         <option value="basic" selected="True">Hide Advanced Options</option>
    24. 

  24.         <option value="advanced">Show Advanced Options</option>
    25. 

  25.       </param>
    26. 

  26.       <when value="basic">
    27. 

  27.         <param name="input_config_file" type="select" label="Select a pre-defined configuration file">
    28. 

  28.           <options from_data_table="ccat_configurations">
    29. 

  29.             <validator type="no_options" message="No configurations are available"/>
    30. 

  30.           </options>
    31. 

  31.         </param>
    32. 

  32.       </when>
    33. 

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

  34.         <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
    35. 

  35.         <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
    36. 

  36.         <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
    37. 

  37.         <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
    38. 

  38.           <option value="1">Transition from sense strand to anti-sense strand</option>
    39. 

  39.           <option value="0" selected="True">Local maximum of read-enrichment profile</option>
    40. 

  40.         </param>
    41. 

  41.         <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
    42. 

  42.         <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
    43. 

  43.         <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
    44. 

  44.         <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
    45. 

  45.         <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
    46. 

  46.       </when>
    47. 

  47.     </conditional>
    48. 

  48.   </inputs>
    49. 

  49.   <outputs>
    50. 

  50.     <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
    51. 

  51.       <actions>
    52. 

  52.         <action type="metadata" name="chromCol" default="1"/>
    53. 

  53.         <action type="metadata" name="startCol" default="3"/>
    54. 

  54.         <action type="metadata" name="endCol" default="4"/>
    55. 

  55.       </actions>
    56. 

  56.     </data>
    57. 

  57.     <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
    58. 

  58.       <actions>
    59. 

  59.         <action type="metadata" name="chromCol" default="1"/>
    60. 

  60.         <action type="metadata" name="startCol" default="3"/>
    61. 

  61.         <action type="metadata" name="endCol" default="4"/>
    62. 

  62.       </actions>
    63. 

  63.     </data>
    64. 

  64.     <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
    65. 

  65.       <actions>
    66. 

  66.         <action type="metadata" name="chromCol" default="1"/>
    67. 

  67.         <action type="metadata" name="startCol" default="3"/>
    68. 

  68.         <action type="metadata" name="endCol" default="4"/>
    69. 

  69.       </actions>
    70. 

  70.     </data>
    71. 

  71.     <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
    72. 

  72.   </outputs>
    73. 

  73.   <configfiles>
    74. 

  74.     <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
    75. 

  75. fragmentSize	${options_type[ 'fragment_size' ]}
    76. 

  76. slidingWinSize	${options_type[ 'sliding_window_size' ]}
    77. 

  77. movingStep	${options_type[ 'moving_step' ]}
    78. 

  78. isStrandSensitiveMode	${options_type[ 'is_strand_sensitive_mode' ]}
    79. 

  79. minCount	${options_type[ 'min_count' ]}
    80. 

  80. outputNum	${options_type[ 'output_num' ]}
    81. 

  81. randomSeed	${options_type[ 'random_seed' ]}
    82. 

  82. minScore	${options_type[ 'min_score' ]}	
    83. 

  83. bootstrapPass	${options_type[ 'bootstrap_pass' ]}
    84. 

  84. #end if</configfile>
    85. 

  85.   </configfiles>
    86. 

  86.   <tests>
    87. 

  87.     <test>
    88. 

  88.       <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
    89. 

  89.       <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
    90. 

  90.       <param name="options_type_selector" value="advanced" />
    91. 

  91.       <param name="fragment_size" value="200" />
    92. 

  92.       <param name="sliding_window_size" value="500" />
    93. 

  93.       <param name="moving_step" value="50" />
    94. 

  94.       <param name="is_strand_sensitive_mode" value="0" />
    95. 

  95.       <param name="min_count" value="4" />
    96. 

  96.       <param name="output_num" value="100000" />
    97. 

  97.       <param name="random_seed" value="123456" />
    98. 

  98.       <param name="min_score" value="5.0" />
    99. 

  99.       <param name="bootstrap_pass" value="50" />
    100. 

  100.       <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
    101. 

  101.       <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
    102. 

  102.       <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />
    103. 

  103.       <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
    104. 

  104.     </test>
    105. 

  105.     <test>
    106. 

  106.       <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
    107. 

  107.       <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
    108. 

  108.       <param name="options_type_selector" value="basic" />
    109. 

  109.       <param name="input_config_file" value="ccat_3.0_histone_config" />
    110. 

  110.       <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
    111. 

  111.       <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
    112. 

  112.       <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
    113. 

  113.       <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
    114. 

  114.     </test>
    115. 

  115.     <!-- Test below gives different answers on different architectures, 
    116. 

  116.     e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386 
    117. 

  117.     slidingWinSize was fixed to be 1000, default as per readme.txt
    118. 

  118.     -->
    119. 

  119.     <!--
    120. 

  120.     <test>
    121. 

  121.       <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
    122. 

  122.       <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
    123. 

  123.       <param name="options_type_selector" value="basic" />
    124. 

  124.       <param name="input_config_file" value="ccat_3.0_histone_config_readme" />
    125. 

  125.       <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />
    126. 

  126.       <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />
    127. 

  127.       <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" />
    128. 

  128.       <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />
    129. 

  129.     </test>
    130. 

  130.   -->
    131. 

  131.   </tests>
    132. 

  132.   <help>
    133. 

  133. **What it does**
    134. 

  134. 

  135. This tool allows ChIP-seq peak/region calling using CCAT.
    136. 

  136. 

  137. View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.
    138. 

  138. 

  139. ------
    140. 

  140. 

  141. **Citation**
    142. 

  142. 

  143. For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
    144. 

  144. 

  145. If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
    146. 

  146. 

  147.   </help>
    148. 

  148. </tool>
    149.