Mercurial > repos > miller-lab > genome_diversity

annotate map_ensembl_transcripts.xml @ 17:a3af29edcce2

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Uploaded Miller Lab Devshed version a51c894f5bed
author miller-lab
date Fri, 28 Sep 2012 11:57:18 -0400
parents 8ae67e9fb6ff
children d6b961721037
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1 <tool id="gd_new_oscar" name="Get Pathways" version="1.0.0">
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2 <description>: Look up KEGG pathways for given Ensembl transcripts</description>
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3
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4 <command interpreter="python">
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5 rtrnKEGGpthwfENSEMBLTc.py
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6 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.oscar.loc"
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7 "--species=${input.metadata.dbkey}"
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8 "--input=${input}"
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9 "--posENSEMBLclmn=${ensembl_col}"
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10 "--output=${output}"
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11 </command>
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12
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13 <inputs>
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14 <param name="input" type="data" format="tabular" label="Table" />
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15 <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript code" />
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16 </inputs>
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17
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18 <outputs>
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19 <data name="output" format="tabular" />
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20 </outputs>
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21
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22 <!--
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23 <tests>
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24 <test>
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25 <param name="input" value="test_in/ensembl.tabular" ftype="tabular">
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26 <metadata name="dbkey" value="canFam2" />
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27 </param>
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28 <param name="ensembl_col" value="1" />
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29
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30 <output name="output" file="test_out/map_ensembl_transcripts/map_ensembl_transcripts.tabular" />
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31 </test>
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32 </tests>
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33 -->
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34
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35 <help>
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36
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37 **What it does**
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38
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39 Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes.
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40
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41 </help>
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42 </tool>