view isoem2_isode2/isoDE.xml @ 11:630d5a01ef13 draft

Minor change in IsoDE2 interface

<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="Significance level" type="float" value="0.05" help="Desired significance level for which a conservative (reliable) fold change 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. 

**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 Significance level 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- Conservative log_2(FC) : conservative estimate of fold change in log base 2. 
*               For the confidence level as input, 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. 0 indicates that no change was detected.
* 3- log_2(condition 2 FPKM (or TPM)/condition 1 FPKM(or TPM)) based on IsoEM2 run without bootstrapping (average FPKM or TPM if replicates used)
* 4- condition 1 FPKM (or TPM) based on IsoEM2 run without bootstrapping (average if replicates used)
* 5- condition 2 FPKM (or TPM) based on IsoEM2 run without bootstrapping (average if replicates used)
 

</help>
</tool>