Mercurial > repos > dktanwar > fgsea_test

comparison GSEA.xml @ 1:23f1abdec8d1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dktanwar
date Mon, 18 Dec 2017 21:10:26 -0500
parents
children
comparison
equal deleted inserted replaced
0:3a53b8e91ede 1:23f1abdec8d1
1 <tool id="GSEA" name="Gene Set Enrichment Analysis" version="0.1.0">
2
3 <requirements>
4 <requirement type="package" version="1.4.0">bioconductor-fgsea</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <!-- required for alpha function used with plotMD -->
7 <requirement type="package" version="0.12.13">r-rcpp</requirement>
8 <requirement type="package" version="1.10.4">r-data.table</requirement>
9 </requirements>
10
11 <command detect_errors="exit_code"><![CDATA[
12 Rscript '$__tool_directory__/GSEA.R' --input1 '$edgeR_output' --input2 '$Pathway_database' --output '$output'
13 ]]></command>
14 <inputs>
15 <param type="data" name="edgeR_output" format="tabular" />
16 <param type="data" name="Pathway_database" format="txt" />
17 </inputs>
18 <outputs>
19 <data name="output" format="txt" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="edgeR_output" value="input.tab"/>
24 <param name="Pathway_database" value="mouse.gmt"/>
25 <output name="output" file="GSEA_results.txt"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 Write the tool help section here.
30 ]]></help>
31 <citations>
32 <citation type="bibtex">
33 @misc{github01_mismatch_removal,
34 author = {LastTODO, FirstTODO},
35 year = {TODO},
36 title = {01_mismatch_removal},
37 publisher = {GitHub},
38 journal = {GitHub repository},
39 url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
40 }</citation>
41 </citations>
42 </tool>