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/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  <description>Control-based ChIP-seq Analysis Tool</description>
  3  <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' 
  4  #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
  5  '$input_advanced_config_file' 
  6  #else:
  7  '${ options_type.input_config_file.fields.path }'
  8  #end if
  9  'CCAT in Galaxy' 
 10  '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command>
 11  <requirements>
 12    <requirement type="binary" version="3.0">CCAT</requirement>
 13  </requirements>
 14  <inputs>
 15    <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" >
 16      <validator type="unspecified_build" />
 17    </param>
 18    <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >
 19      <validator type="unspecified_build" />
 20    </param>
 21    <conditional name="options_type">
 22      <param name="options_type_selector" type="select" label="Advanced Options">
 23        <option value="basic" selected="True">Hide Advanced Options</option>
 24        <option value="advanced">Show Advanced Options</option>
 25      </param>
 26      <when value="basic">
 27        <param name="input_config_file" type="select" label="Select a pre-defined configuration file">
 28          <options from_data_table="ccat_configurations">
 29            <validator type="no_options" message="No configurations are available"/>
 30          </options>
 31        </param>
 32      </when>
 33      <when value="advanced">
 34        <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
 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        <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
 37        <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
 38          <option value="1">Transition from sense strand to anti-sense strand</option>
 39          <option value="0" selected="True">Local maximum of read-enrichment profile</option>
 40        </param>
 41        <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
 42        <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
 43        <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
 44        <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
 45        <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
 46      </when>
 47    </conditional>
 48  </inputs>
 49  <outputs>
 50    <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
 51      <actions>
 52        <action type="metadata" name="chromCol" default="1"/>
 53        <action type="metadata" name="startCol" default="3"/>
 54        <action type="metadata" name="endCol" default="4"/>
 55      </actions>
 56    </data>
 57    <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
 58      <actions>
 59        <action type="metadata" name="chromCol" default="1"/>
 60        <action type="metadata" name="startCol" default="3"/>
 61        <action type="metadata" name="endCol" default="4"/>
 62      </actions>
 63    </data>
 64    <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
 65      <actions>
 66        <action type="metadata" name="chromCol" default="1"/>
 67        <action type="metadata" name="startCol" default="3"/>
 68        <action type="metadata" name="endCol" default="4"/>
 69      </actions>
 70    </data>
 71    <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
 72  </outputs>
 73  <configfiles>
 74    <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
 75fragmentSize	${options_type[ 'fragment_size' ]}
 76slidingWinSize	${options_type[ 'sliding_window_size' ]}
 77movingStep	${options_type[ 'moving_step' ]}
 78isStrandSensitiveMode	${options_type[ 'is_strand_sensitive_mode' ]}
 79minCount	${options_type[ 'min_count' ]}
 80outputNum	${options_type[ 'output_num' ]}
 81randomSeed	${options_type[ 'random_seed' ]}
 82minScore	${options_type[ 'min_score' ]}	
 83bootstrapPass	${options_type[ 'bootstrap_pass' ]}
 84#end if</configfile>
 85  </configfiles>
 86  <tests>
 87    <test>
 88      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
 89      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
 90      <param name="options_type_selector" value="advanced" />
 91      <param name="fragment_size" value="200" />
 92      <param name="sliding_window_size" value="500" />
 93      <param name="moving_step" value="50" />
 94      <param name="is_strand_sensitive_mode" value="0" />
 95      <param name="min_count" value="4" />
 96      <param name="output_num" value="100000" />
 97      <param name="random_seed" value="123456" />
 98      <param name="min_score" value="5.0" />
 99      <param name="bootstrap_pass" value="50" />
100      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
101      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
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      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
104    </test>
105    <test>
106      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
107      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
108      <param name="options_type_selector" value="basic" />
109      <param name="input_config_file" value="ccat_3.0_histone_config" />
110      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
111      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
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      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
114    </test>
115    <!-- Test below gives different answers on different architectures, 
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    slidingWinSize was fixed to be 1000, default as per readme.txt
118    -->
119    <!--
120    <test>
121      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
122      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
123      <param name="options_type_selector" value="basic" />
124      <param name="input_config_file" value="ccat_3.0_histone_config_readme" />
125      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />
126      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />
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      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />
129    </test>
130  -->
131  </tests>
132  <help>
133**What it does**
134
135This tool allows ChIP-seq peak/region calling using CCAT.
136
137View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.
138
139------
140
141**Citation**
142
143For 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
145If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
146
147  </help>
148</tool>