annotate data_filtering.xml @ 0:0e37e5b73273 draft

Initial commit

<tool id="dataFilter" name="Data Filtering" version="0.9">
    <description>Filter IMGT Summary dataset</description>
    <requirements>
      <requirement type="package" version="0.19">pandas</requirement>
    </requirements>
    <command interpreter="python">data_filtering.py $input $TCR_or_BCR $Vfun $spChar $prod $delCF $threshold $Vg.Vgid $clen.cdr3len1 $cdp.cdr3part $filterin_file $filterout_file $summary_file $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="filterin_file" format="tabular" label="${process_id}_filterin" />
        <data name="filterout_file" format="tabular" label="${process_id}_filterout" />
        <data name="summary_file" format="tabular" label="${process_id}_filterSummary" />
    </outputs>
    <help>
This tool filters an IMGT Summary dataset based on a combination of criteria.
  </help>
</tool>