Mercurial > repos > iuc > humann_unpack_pathways

annotate humann_unpack_pathways.xml @ 0:c3d043160f09 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
author iuc
date Wed, 12 May 2021 09:07:12 +0000
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c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <tool id="humann_unpack_pathways" name="Unpack pathway abundances" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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2 <description>to show the genes for each</description>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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3 <macros>
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4 <import>macros.xml</import>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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5 </macros>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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6 <expand macro="edam_ontology"/>
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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[
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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10 humann_unpack_pathways
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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11 --input-genes '$input_genes'
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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12 --input-pathways '$input_pathways'
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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13 #if $gene_mapping
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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14 --gene-mapping '$gene_mapping'
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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15 #end if
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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16 #if $pathway_mapping
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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17 --pathway-mapping '$pathway_mapping'
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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18 #end if
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19 $remove_taxonomy
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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20 --output '$output'
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21 ]]></command>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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22 <inputs>
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23 <param argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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24 <param argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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25 <param argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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26 <param argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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27 <param argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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28 </inputs>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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29 <outputs>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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30 <data format="tabular" name="output"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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31 </outputs>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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32 <tests>
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33 <test expect_num_outputs="1">
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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"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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36 <param name="remove_taxonomy" value=""/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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37 <output name="output" ftype="tabular">
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38 <assert_contents>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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39 <has_text text="humann_Abundance"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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40 <has_text text="PWY-4203|unclassified|UniRef90_Q6XMI3"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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41 <has_n_columns n="2"/>
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42 </assert_contents>
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43 </output>
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44 </test>
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45 <test expect_num_outputs="1">
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46 <param name="input_genes" value="demo_genefamilies.tsv"/>
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47 <param name="input_pathways" value="demo_pathabundance.tsv"/>
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48 <param name="remove_taxonomy" value="--remove-taxonomy"/>
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49 <output name="output" ftype="tabular">
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50 <assert_contents>
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51 <has_text text="humann_Abundance"/>
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52 <has_text text="PWY-4203|UniRef90_Q6XMI3"/>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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53 <has_n_columns n="2"/>
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54 </assert_contents>
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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55 </output>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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59 @HELP_HEADER@
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60
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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61 This tool unpacks the pathways to show the genes for each.
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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62
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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63 It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.
c3d043160f09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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64 ]]></help>
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65 <expand macro="citations"/>
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66 </tool>