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comparison map_ensembl_transcripts.xml @ 12:4b6590dd7250

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author miller-lab
date Wed, 12 Sep 2012 17:10:26 -0400
parents 2c498d40ecde
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11:d4ec09e8079f 12:4b6590dd7250
1 <tool id="gd_new_oscar" name="Map" version="1.0.0">
2 <description>Ensembl transcripts to KEGG pathways</description>
3
4 <command interpreter="python">
5 rtrnKEGGpthwfENSEMBLTc.py
6 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.oscar.loc"
7 "--species=${input.metadata.dbkey}"
8 "--input=${input}"
9 "--posENSEMBLclmn=${ensembl_col}"
10 "--output=${output}"
11 </command>
12
13 <inputs>
14 <param name="input" type="data" format="tabular" label="Table" />
15 <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript code" />
16 </inputs>
17
18 <outputs>
19 <data name="output" format="tabular" />
20 </outputs>
21
22 <!--
23 <tests>
24 <test>
25 <param name="input" value="test_in/ensembl.tabular" ftype="tabular">
26 <metadata name="dbkey" value="canFam2" />
27 </param>
28 <param name="ensembl_col" value="1" />
29
30 <output name="output" file="test_out/map_ensembl_transcripts/map_ensembl_transcripts.tabular" />
31 </test>
32 </tests>
33 -->
34
35 <help>
36 **What it does**
37
38 Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes.
39 </help>
40 </tool>