view ngs_filtering.xml @ 12:cdf95051bc55 draft default tip

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<tool id="ngsFilt" name="IMGT Report Filtering" version="0.9" profile="15.10">
  <description>Filter IMGT Summary Data</description>
  <command interpreter="python">ngs_filtering.py $input $TCR_or_BCR $Vfun $spChar $prod $delCF $threshold $Vg.Vgid $clen.cdr3len1 $cdp.cdr3part $filtin $filtout $summ $Jg.Jgid $Dg.Dgid $clen.cdr3len2 $process_id
	
  </command>
  <inputs>
    <param format="txt" name="input" type="data" label="IMGT Summary Output"/>
	<param format="txt" name="process_id" type="text" label="Process ID"/>
	<param name="TCR_or_BCR" type="select" label="T-cell or B-cell option">
    <option value="TCR">T-cell</option>
    <option value="BCR">B-cell</option>
    </param>
	<param name="Vfun" type="select" label="Only Take Into Account Fuctional V-GENE? ">
	<option value="y">yes</option>
      <option value="n">no</option>
      </param>

	<param name="spChar" type="select" label="Only Take Into Account CDR3 with no Special Characters (X,*,#)? ">
     <option value="y">yes</option> 
	<option value="n">no</option>
      </param>

  <param name="prod" type="select" label="Only Take Into Account Productive Sequences? ">
     <option value="y">yes</option> 
	<option value="n">no</option>
      </param>

  <param name="delCF" type="select" label="Only Take Into Account CDR3 with valid start/end landmarks? ">
	<option value="y">yes</option>
      <option value="n">no</option>
      </param>

    <param name="threshold" type="float" size="3" value="0" min="0" max="100" label="V-REGION identity %" />
  
  <conditional name="Vg">
	
	<param name="Vg_select" type="select" label="Select Specific V gene?">
        <option value="y">Yes</option>
		<option value="n" selected="true">No</option>
    </param>
	
	<when value="y">
          <param format="txt" name="Vgid" type="text" label="Type V gene"/>
     </when>
	
	<when value="n">
		<param name="Vgid" type="hidden" value="null" />
     </when>

	 </conditional>
	 
	  <conditional name="Jg">
	
	<param name="Jg_select" type="select" label="Select Specific J gene?">
        <option value="y">Yes</option>
		<option value="n" selected="true">No</option>
    </param>
	
	<when value="y">
          <param format="txt" name="Jgid" type="text" label="Type J gene"/>
     </when>
	
	<when value="n">
		<param name="Jgid" type="hidden" value="null" />
     </when>

	 </conditional>
	 
	 <conditional name="Dg">
	
	<param name="Dg_select" type="select" label="Select Specific D gene?">
        <option value="y">Yes</option>
		<option value="n" selected="true">No</option>
    </param>
	
	<when value="y">
          <param format="txt" name="Dgid" type="text" label="Type D gene"/>
     </when>
	
	<when value="n">
		<param name="Dgid" type="hidden" value="null" />
     </when>

	 </conditional>
	 
	 
	
	<conditional name="clen">

	<param name="clen_select" type="select" label="Select CDR3 length range?">
        <option value="y">Yes</option>
		<option value="n" selected="true">No</option>
    </param>

	<when value="y">
		<param name="cdr3len1" type="integer" size="3" value="0" min="0" max="100" label="CDR3 Length Lower Threshold" />
		<param name="cdr3len2" type="integer" size="3" value="0" min="0" max="100" label="CDR3 Length Upper Threshold" />
	</when>

	<when value="n">
		<param name="cdr3len1" type="hidden" value="null" />
		<param name="cdr3len2" type="hidden" value="null" />
	</when>

	</conditional>
	
	<conditional name="cdp">
	
	<param name="cdp_select" type="select" label="Only select CDR3 containing specific amino-acid sequence?">
        <option value="y">Yes</option>
		<option value="n" selected="true">No</option>
    </param>
	
	<when value="y">
    <param format="txt" name="cdr3part" type="text" label="Type specific amino-acid sequence"/>
	</when>
	
	<when value="n">
		<param name="cdr3part" type="hidden" value="null" />
	</when>
	</conditional>
  
  </inputs>
  
  
  <outputs>
	<data name="filtin" format="tabular" 	label="${process_id}_filterin"/>
	<data name="filtout" format="tabular" 	label="${process_id}_filterout"/>
	<data name="summ" format="tabular" 	label="${process_id}_Summary"/>


  </outputs>


  <help>
This tool filters IMGT Summary Data based on a combination of criteria.
  </help>

</tool>