annotate isoem2_isode2/isoDE.xml @ 18:c6d2dbdf0a4d draft

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<tool id="isoDE" name="IsoDE2">
  <description>Computes differentially expressed isoforms and genes based on bootstrap samples generated by IsoEM2 </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="sampleName1"  size="10" type="text"  label="Name for Condition 1" value="Condition1" help="Output files label"/>

    <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 name="sampleName2"  size="10" type="text"  label="Name for Condition 2" value="Condition2" help="Output files label"/>

    <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="${sampleName1}.vs.${sampleName2} isoDE gene fpkm "  />
    <data format="tabular" name="isoformFPKM" label="${sampleName1}.vs.${sampleName2} isoDE isoform fpkm "  />
    <data format="tabular" name="geneTPM" label="${sampleName1}.vs.${sampleName2} isoDE gene tpm "  />
    <data format="tabular" name="isoformTPM" label="${sampleName1}.vs.${sampleName2} isoDE isoform tpm "  />
  </outputs>

<help>
**What it does**

IsoDE2 computes isoforms and genes that are differentially expressed between two conditions (e.g., treated vs. control). 
The computation is based on the boostrap samples generated by IsoEM2. 

**Input**

* 1- Names for the two conditions (the default values 'Condition 1' and 'Condition 2' will be used in the output file names if these are not specified)
* 2- One or more IsoEM output files (compressed tar files) for each of the two conditions. Multiple files can be used when IsoEM2 is run independently on replicates for each condition.
* 3- Desired significance level for which a reliable fold change level will be reported.
*




**Output**

* Four output files containinag results of isoform and gene differential expression analysis based on both Fragments per Kilobase per Million (FPKM) and Transcripts per Million (TPM) expression levels. The four tab delimited files have identical format with the following fields:
* 1- Isoform/Gene ID
* 2- Confident log_2(FC): the base 2 logarithm of the largest fold change of isoform/gene FPKM/TPM estimates of condition 2 vs condition 1 which is supported by the provided bootstrap samples at the specified significance level. Positive values represent over-expression in Condition 2, while negative values representing over-expression in Condition 1. A zero value in this field indicates that no significant change was detected.
* 3- Single run log2(FC): the base 2 logarithm of the ratio between expression levels estimated by IsoEM2 for Condition 2 and Condition 1 (ratio between mean estimates in case replicates are provided for the two conditions).
* 4- Condition 1 FPKM or TPM: the IsoEM2 expression level estimated for Condition 1 (mean value in case of replicates).
* 5- Condition 2 FPKM or TPM: the IsoEM2 expression level estimated for Condition 2 (mean value in case of replicates).
*

</help>
</tool>