comparison rgedgeR/rgedgeRpaired.xml @ 8:a4edc1360ea9 draft

Uploaded

7:8c0405de0695

      <requirement type="package" version="9.07">ghostscript</requirement>
  </requirements>
  
  <command interpreter="python">
     rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" 
    --output_dir "$html_file.files_path" --output_html "$html_file" --output_tab "$outtab" --make_HTML "yes"
  </command>
  <inputs>
    <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
       help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
    <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" 

            <option value="none">no control for multiple tests</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
         <filter>edgeR.doedgeR == "T"</filter>
    </data>
    <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
         <filter>DESeq2.doDESeq2 == "T"</filter>
    </data>
    <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
         <filter>doVoom == "T"</filter>
    </data>
    <data format="html" name="html_file" label="${title}.html"/>

 <param name='fdrthresh' value="0.05" />
 <param name='control_name' value='control' />
 <param name='subjectids' value='' />
  <param name='Treat_cols' value='3,4,5,9' />
 <param name='Control_cols' value='2,6,7,8' />
 <output name='outtab' file='edgeRtest1out.xls' compare='diff' />
 <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
</test>
</tests>

<configfiles>

Input =  "$input1"
TreatmentName = "$treatment_name"
TreatmentCols = "$Treat_cols"
ControlName = "$control_name"
ControlCols= "$Control_cols"
outputfilename = "$outtab"
org = "$input1.dbkey"
if (org == "") { org = "hg19"}
fdrtype = "$fdrtype"
fdrthresh = $fdrthresh
useNDF = "$useNDF"

8:a4edc1360ea9

      <requirement type="package" version="9.07">ghostscript</requirement>
  </requirements>
  
  <command interpreter="python">
     rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" 
    --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
  </command>
  <inputs>
    <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
       help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
    <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" 

            <option value="none">no control for multiple tests</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
         <filter>doedgeR == "T"</filter>
    </data>
    <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
         <filter>doDESeq2 == "T"</filter>
    </data>
    <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
         <filter>doVoom == "T"</filter>
    </data>
    <data format="html" name="html_file" label="${title}.html"/>

 <param name='fdrthresh' value="0.05" />
 <param name='control_name' value='control' />
 <param name='subjectids' value='' />
  <param name='Treat_cols' value='3,4,5,9' />
 <param name='Control_cols' value='2,6,7,8' />
 <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
 <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
</test>
</tests>

<configfiles>

Input =  "$input1"
TreatmentName = "$treatment_name"
TreatmentCols = "$Treat_cols"
ControlName = "$control_name"
ControlCols= "$Control_cols"
org = "$input1.dbkey"
if (org == "") { org = "hg19"}
fdrtype = "$fdrtype"
fdrthresh = $fdrthresh
useNDF = "$useNDF"