Mercurial > repos > rico > test_single_file
changeset 9:2ca8873daedd
Uploaded
| author | rico |
|---|---|
| date | Thu, 05 Apr 2012 15:15:09 -0400 |
| parents | 5f6ee4f6fd0b |
| children | ea6353a54fda |
| files | map_ensembl_transcripts.xml |
| diffstat | 1 files changed, 38 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/map_ensembl_transcripts.xml Thu Apr 05 15:15:09 2012 -0400 @@ -0,0 +1,38 @@ +<tool id="gd_new_oscar" name="Map" version="1.0.0"> + <description>Ensembl transcripts to KEGG pathways</description> + + <command interpreter="python"> + rtrnKEGGpthwfENSEMBLTc.py + "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.oscar.loc" + "--species=${input.metadata.dbkey}" + "--input=${input}" + "--posENSEMBLclmn=${ensembl_col}" + "--output=${output}" + </command> + + <inputs> + <param name="input" type="data" format="tabular" label="Table" /> + <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript code" /> + </inputs> + + <outputs> + <data name="output" format="tabular" /> + </outputs> + + <tests> + <test> + <param name="input" value="genome_diversity/test_in/ensembl.tabular" ftype="tabular"> + <metadata name='dbkey' value='canFam2' /> + </param> + <param name="ensembl_col" value="1" /> + + <output name="output" file="genome_diversity/test_out/map_ensembl_transcripts/map_ensembl_transcripts.tabular" /> + </test> + </tests> + + <help> +**What it does** + +Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes. + </help> +</tool>