view createControlSubSet_wrapper.xml @ 3:342a53ff1fd6 draft default tip

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<!--create control subset - developed by Jocelyn Brayet <[e-mail]>
Copyright (C) 2015  Institut Curie

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.-->
<tool id="createControlSubset" name="Get Subset for ChIP Control" version="1.0">
  <description> </description>
  <requirements>
    <container type="docker">institutcuriengsintegration/controlsubset:1.0</container>
  </requirements>
  <command interpreter="bash">
#if $input_type.input_type_selector == "bam" #createControlSubSet_wrapper.sh -f $inputfile -c $controlfile -t $input_type.input_type_selector -o $BAMcontrolOutBAM -s $BAMsampleOutBAM -q $if_Process_Sample -p "No" #elif $input_type.input_type_selector == "sam" #createControlSubSet_wrapper.sh -f $inputfile -c $controlfile -t $input_type.input_type_selector -o $SAMcontrolOut -s $SAMsampleOut -q $if_Process_Sample #else #createControlSubSet_wrapper.sh -f $inputfile -c $controlfile -t $input_type.input_type_selector -o $ELANDcontrolOut -s $ELANDsampleOut -q $if_Process_Sample  #end if
 </command>

   <inputs>
    <conditional name="input_type">
    <param name="input_type_selector" type="select" label="Alignment Format">
        <option value="eland" selected="true">Eland</option>
        <option value="sam">SAM</option>
        <option value="bam">BAM</option>
    </param>
    <when value="eland">
    <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="eland"/>
    <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="eland"/>

    </when>
    <when value="sam">
    <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="sam"/>
    <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="sam"/>

    </when>
    <when value="bam">
    <param name="inputfile" type="data" label="ChIP-Seq Tag File" value="ChIP-Seq Tag File" format="bam"/>
    <param name="controlfile" type="data" label="Control Tag File" value="Control Tag File" format="bam"/>
 <!--   <param name="if_OutPut_In_Sam" type="boolean" label="Do you want to get the output in SAM instead of BAM?" help="recommended if you want to run FindPeaks on it" truevalue="Yes" falsevalue="No" checked="False"/>
-->
    </when>
    </conditional>


    <param name="if_Process_Sample" type="boolean" label="Do you want to filter duplicates in the ChIP dataset?" truevalue="Yes" falsevalue="No" checked="False"/>


  </inputs>
  <outputs>
    <data name="ELANDcontrolOut" format="eland" label="Subset for Control">
    <filter>(input_type['input_type_selector'] == 'eland')</filter>
    </data>
    <data name="SAMcontrolOut" format="sam" label="Subset for Control">
    <filter>(input_type['input_type_selector'] == 'sam')</filter>
    </data>

    <data name="BAMcontrolOutBAM" format="bam" label="Subset for Control">
    <filter>(input_type['input_type_selector'] == 'bam')</filter>    
    </data>


    <data name="ELANDsampleOut" format="eland" label="Subset for ChIP">    
      <filter>if_Process_Sample == True</filter>
      <filter>(input_type['input_type_selector'] == 'eland')</filter>
    </data>
    <data name="SAMsampleOut" format="sam" label="Subset for ChIP">    
      <filter>if_Process_Sample == True</filter>
      <filter>(input_type['input_type_selector'] == 'sam')</filter>
    </data>

  <data name="BAMsampleOutBAM" format="bam" label="Subset for ChIP">    
      <filter>if_Process_Sample == True</filter>
      <filter>(input_type['input_type_selector'] == 'bam')</filter>
    </data>

  </outputs>
  <help>
**What it does**

This tool does preprocessing of ChIP-seq aligned reads before calling FindPeaks:

Filter out dulpicates from the SAMPLE (optional) and create a CONTROL dataset w/o duplicates with the same number of reads as in the SAMPLE

Only eland, sam and bam files are accepted.

  </help>
</tool>