annotate SMART/DiffExpAnal/deseq.xml @ 31:0ab839023fe4

Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
1 <tool id="DESEQ" name="DESEQ for differential expression analysis">
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
2 <description>Differential expression analysis for reads count data</description>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
3 <command interpreter="bash"> deseq.sh $inputFile $header $withOutReplicates $outHTML $outHTML.files_path $outComplete $outUP $outDown 2> $log </command>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
4
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
5 <inputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
6 <param name="inputFile" type="data" label="Input File list" format="txt"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
7 <param name="header" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If there is a header for your count files, please choose this case."/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
8 <param name="withOutReplicates" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If your data has not replicates, please choose this case."/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
9
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
10 </inputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
11
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
12 <outputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
13 <data format="HTML" name="outHTML" label="[DESEQ] Output HTML File" help="This output file shows all results images by DESeq analysis"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
14 <data format="tabular" name="outComplete" label="[DESEQ] Output complete File"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
15 <data format="tabular" name="outUP" label="[DESEQ] Output up File" help="This output file shows the genes of group1 which are overexpressed than those of group2"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
16 <data format="tabular" name="outDown" label="[DESEQ] Output down File" help="This output file shows the genes of group1 which are less expressed than those of group2"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
17 <data format="txt" name="log" label="[DESEQ] Output log File"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
18 </outputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
19
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
20 <help>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
21 </help>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
22 </tool>