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1 <tool id="gd_pathway_image" name="Generate" version="1.0.0">
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2 <description>KEGG pathway images</description>
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3
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4 <command interpreter="python">
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5 mkpthwpng.py
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6 "--input=${input}"
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7 "--output=${output}"
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8 "--KEGGpath=${pathway}"
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9 "--posKEGGclmn=${input.metadata.kegg_path}"
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10 "--KEGGgeneposcolmn=${input.metadata.kegg_gene}"
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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="gd_sap" label="Table">
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15 <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata. Click the pencil icon in the history item to edit/save the metadata attributes" />
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16 </param>
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17 <param name="pathway" type="select">
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18 <options from_file="gd.pathways.txt">
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19 <column name="value" index="1"/>
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20 <column name="name" index="2"/>
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21 <filter type="data_meta" ref="input" key="dbkey" column="0" separator="\t" />
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22 </options>
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23 </param>
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24 </inputs>
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25
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26 <outputs>
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27 <data name="output" format="png" />
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28 </outputs>
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29
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30 <tests>
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31 <test>
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32 <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" />
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33 <param name="pathway" value="cfa05214" />
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34 <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" />
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35 </test>
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36 </tests>
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37
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38 <help>
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39 **What it does**
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40
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41 This tool produces an image of an input KEGG pathway, highlighting the
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42 modules representing genes in an input list. NOTE: a given gene can
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43 be assigned to multiple modules, and different genes can be assigned to
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44 the same module.
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45 </help>
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46 </tool>
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