annotate isoDE.xml @ 1:babf45f7c9a3 draft

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<tool id="isoDE" name="IsoDE2">
  <description>Compute gene Differential Expression based on IsoEM2 output </description>
  <command interpreter="bash">isoDE2.sh
      -c1
      $condition1
      #for $r in $condition1replicates
        ${r.c1Rep}
      #end for
      -c2
      $condition2
      #for $r in $condition2replicates
        ${r.c2Rep}
      #end for
      -pval $pval
      -geneFPKMout $geneFPKM
	-geneTPMout $geneTPM
	-isoFPKMout $isoformFPKM  
	-isoTPMout $isoformTPM
 </command>

  <inputs>
  <param name="condition1" type="data" label="Select data for Condition 1" format="gz" help="Condition 1 isoEM2 compressed output file"/>
<!--
    <param format="toolshed.gz" name="condition1" type="data" label="Select data for Condition 1" help="Condition 1 isoEM2 compressed output file"/>
-->
    <repeat name="condition1replicates" title="Replicates for Condition 1">
      <param name="c1Rep" label="Add replicate" type="data" format="gz" data_ref="condtion1" />
    </repeat>

    <param format="gz" name="condition2" type="data" label="Select data for Condition 2"  help="Condition 2 isoEM2 compressed output file"/>
<!--
    <param  format="toolshed.gz" name="condition2" type="data" label="Select data for Condition 2" help="Condition 2 IsoEM2 compressed output file"/>
-->
    <repeat name="condition2replicates" title="Replicates for Condition 2">
      <param format="gz" name="c2Rep" label="Add replicate" type="data" data_ref="condtion2" />
    </repeat>


    <param name="pval" label="p-value" type="float" value="0.05" help="Desired p-value to for which a reliable fold change level will be reported" />

  </inputs>
  <outputs>
    <data format="tabular" name="geneFPKM" label="isoDE gene fpkm"  />
    <data format="tabular" name="isoformFPKM" label="isoDE isoform fpkm"  />
    <data format="tabular" name="geneTPM" label="isoDE gene tpm"  />
    <data format="tabular" name="isoformTPM" label="isoDE isoform tpm"  />
  </outputs>

<help>
**What it does**

Computes gene and isoform differential expression between two conditions (example tumor and normal) for both Fragment per Kilobase of transcript length per Million 
bases (FPKM) and Transcripts per Million (TPM) values. The computation is based on the boostraping output generated by IsoEM2. The number of bootstrap iterations for 
IsoEM2 should be >= 20 (suggested 200).

**Input**

* - One or more IsoEM output files (compressed tar files) for each of the two conditions. More than one file can be used if there are replicated for either condition
* - Desired p-value to for which a reliable fold change level will be reported
*




**Output**

* four output files containinag results for Gene FPKM DE, Gene TPM DE, Isoform FPKM DE, and Isoform TPM DE. The four files have identical format with the following fields
* 1- Gene/isoform ID
* 2- Reliable log_2(FC) : conservative estimate of fold change in log base 2. 
*               For the confidence level specified by the input p-value, fold change of gene/isoform abundance (FPKM/TPM) in condition 2 compared condition 1 is 
*               at least 2 ^ absoulte value of this field.The sign indicates the direction, +ve means over expressed in condition 2, -ve means underexpressed in
*               condition 1. NDE indicates that no change was detected.
* 3- log_2(condition 1 FPKM (or TPM)/condition 1 FPKM(or TPM)) based on IsoEM2 run without bootstrapping
* 4- condition 1 FPKM (or TPM) based on IsoEM2 run without bootstrapping
* 5- condition 2 FPKM (or TPM) based on IsoEM2 run without bootstrapping


</help>
</tool>