Mercurial > repos > iuc > humann2_unpack_pathways

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 06:51:03 +0000
parents 5ba8bf13acc6
children
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5ba8bf13acc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
iuc
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1 <tool id="humann2_unpack_pathways" name="Unpack pathway abundances to show genes included" version="@WRAPPER_VERSION@.1">
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2 <description></description>
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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3 <macros>
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4 <import>humann2_macros.xml</import>
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5 </macros>
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5ba8bf13acc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
iuc
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6 <expand macro="stdio"/>
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bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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10 humann2_unpack_pathways
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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11 --input-genes '$input_genes'
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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12 --input-pathways '$input_pathways'
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13 #if $gene_mapping
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14 --gene-mapping '$gene_mapping'
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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15 #end if
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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16 #if $pathway_mapping
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17 --pathway-mapping '$pathway_mapping'
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18 #end if
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19 $remove_taxonomy
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20 --output '$output'
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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21 ]]></command>
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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22 <inputs>
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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23 <param name="input_genes" argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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24 <param name="input_pathways" argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
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25 <param name="gene_mapping" argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
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26 <param name="pathway_mapping" argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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27 <param name="remove_taxonomy" argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
bee645f015fd planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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28 </inputs>
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29 <outputs>
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30 <data format="tsv" name="output" label="${tool.name} on ${on_string}" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input_genes" value="demo_genefamilies.tsv"/>
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35 <param name="input_pathways" value="demo_pathabundance.tsv"/>
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36 <param name="remove_taxonomy" value=""/>
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37 <output name="output" md5="993534d3e8fea242066352a0e4d67c8a"/>
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38 </test>
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39 <test>
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40 <param name="input_genes" value="demo_genefamilies.tsv"/>
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41 <param name="input_pathways" value="demo_pathabundance.tsv"/>
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42 <param name="remove_taxonomy" value="--remove-taxonomy"/>
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43 <output name="output" md5="b145ce760ce656b9e3ddb00d3ff4cf46"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 @HELP_HEADER@
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48
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49 This utility will unpack the pathways to show the genes for each. It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.
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50 ]]></help>
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51 <expand macro="citations"/>
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52 </tool>