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1 <tool id="gd_new_oscar" name="Map" version="1.0.0">
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2 <description>Ensembl transcripts to KEGG pathways</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 **What it does**
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37
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38 Adds the fields KEGG gene codes and KEGG pathways to an input table of ENSEMBL transcript codes.
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39 </help>
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40 </tool>
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