annotate tcga_heatmap.xml @ 5:b2b5f193f5bd draft

Uploaded
author enios
date Wed, 21 Apr 2021 10:54:52 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
1 <tool id="tcga_heatmap" name="TCGA_HEATMAP" >
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
2 <requirements>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
3 <container type="docker">bianca7/lncrna:tcga</container>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
4 </requirements>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
5 <description>Test your signature on TCGA data</description>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
6 <stdio>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
7 <exit_code range="1:" level="fatal" />
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
8 </stdio>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
9 <command><![CDATA[ Rscript /Heatmap1.R -g "$signature" -c "$cancer_type" -R "/$output1" -o "/$output2"
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
10 ]]></command>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
11 <inputs>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
12 <param format="tabular,txt" name="signature" type="data" label="gene signature" />
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
13 <param name="cancer_type" type="text" label="TCGA-cancer project" />
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
14 </inputs>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
15 <outputs>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
16 <data format="pdf" name="output1" label="Heatmap"/>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
17 <data format="html" name="output2" label="Heatmap"/>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
18 </outputs>
b2b5f193f5bd Uploaded
enios
parents:
diff changeset
19 </tool>