<tool id="peakcalling_ccat" name="CCAT" version="0.0.2" profile="20.01">
  <description>Control-based ChIP-seq Analysis Tool</description>
  <requirements>
    <requirement type="package" version="3.0">ccat</requirement>
  </requirements>
  <stdio>
    <regex match="Usage: &lt;library 1 tag file name&gt; &lt;library 2 tag file name&gt; &lt;chromosome length file name&gt; &lt;config file name&gt; &lt;project name&gt;"
           source="both"
           level="fatal"
           description="CLI error" />
     <regex match="tag file error" source="both" level="fatal" description="tag file error" />
  </stdio>
  <command detect_errors="aggressive"><![CDATA[
    echo $in_test_mode && CCAT '$input_tag_file'
      '$input_control_file'
      #if str($in_test_mode) == "no":
        '$chromInfo'
      #else:
        '$__tool_directory__/test-data/genome_length_mm8_chr19.txt'
      #end if
      #if str($options_type['options_type_selector']) == 'advanced':
        '$input_advanced_config_file' 
      #else:
        '${options_type.input_config_file.fields.path}'
      #end if
      CCAT
      | tee '$output_log_file'
  ]]></command>
  <configfiles>
    <configfile name="input_advanced_config_file"><![CDATA[
#if str($options_type['options_type_selector']) == 'advanced':
fragmentSize	${options_type['fragment_size']}
slidingWinSize	${options_type['sliding_window_size']}
movingStep	${options_type['moving_step']}
isStrandSensitiveMode	${options_type['is_strand_sensitive_mode']}
minCount	${options_type['min_count']}
outputNum	${options_type['output_num']}
randomSeed	${options_type['random_seed']}
minScore	${options_type['min_score']}	
bootstrapPass	${options_type['bootstrap_pass']}
#end if
    ]]></configfile>
  </configfiles>
  <inputs>
    <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File"/>
    <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File"/>
    <conditional name="options_type">
      <param name="options_type_selector" type="select" label="Advanced Options">
        <option value="basic" selected="True">Hide Advanced Options</option>
        <option value="advanced">Show Advanced Options</option>
      </param>
      <when value="basic">
        <param name="input_config_file" type="select" label="Select a pre-defined configuration file">
          <options from_data_table="ccat_configurations">
            <validator type="no_options" message="No configurations are available"/>
          </options>
        </param>
      </when>
      <when value="advanced">
        <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
        <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
        <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
        <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
          <option value="1">Transition from sense strand to anti-sense strand</option>
          <option value="0" selected="True">Local maximum of read-enrichment profile</option>
        </param>
        <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
        <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
        <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
        <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
        <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
      </when>
    </conditional>
    <param name="in_test_mode" type="hidden" value="no" />
  </inputs>
  <outputs>
    <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)" from_work_dir="CCAT.significant.peak">
      <actions>
        <action type="metadata" name="chromCol" default="1"/>
        <action type="metadata" name="startCol" default="3"/>
        <action type="metadata" name="endCol" default="4"/>
      </actions>
    </data>
    <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)" from_work_dir="CCAT.significant.region">
      <actions>
        <action type="metadata" name="chromCol" default="1"/>
        <action type="metadata" name="startCol" default="3"/>
        <action type="metadata" name="endCol" default="4"/>
      </actions>
    </data>
    <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)" from_work_dir="CCAT.top100000.peak">
      <actions>
        <action type="metadata" name="chromCol" default="1"/>
        <action type="metadata" name="startCol" default="3"/>
        <action type="metadata" name="endCol" default="4"/>
      </actions>
    </data>
    <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
  </outputs>
  <tests>
    <test>
      <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" />
      <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" />
      <param name="options_type_selector" value="advanced" />
      <param name="fragment_size" value="200" />
      <param name="sliding_window_size" value="300" />
      <param name="moving_step" value="10" />
      <param name="is_strand_sensitive_mode" value="1" />
      <param name="min_count" value="3" />
      <param name="output_num" value="100000" />
      <param name="random_seed" value="123456" />
      <param name="min_score" value="5.0" />
      <param name="bootstrap_pass" value="50" />
      <param name="in_test_mode" value="yes" />
      <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak"/>
      <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />
      <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />
      <output name="output_log_file" file="ES_CTCF_chr19.log" />
    </test>
    <test>
      <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" />
      <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" />
      <param name="options_type_selector" value="basic" />
      <param name="input_config_file" value="config_TF" />
      <param name="in_test_mode" value="yes" />
      <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak" />
      <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />
      <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />
      <output name="output_log_file" file="ES_CTCF_chr19.log" />
    </test>
  </tests>
  <help>
**What it does**

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

View the original CCAT documentation: https://www.comp.nus.edu.sg/~bioinfo/CCAT3.0/
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btq128</citation>
  </citations>
</tool>