annotate humann2_merge_abundance_tables.xml @ 1:bcd414bb721b draft default tip

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 79571d981d7d56657699be8aa24a40a36a8d0ab5-dirty
author bebatut
date Thu, 02 Jun 2016 04:23:09 -0400
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1 <tool id="humann2_merge_abundance_tables" name="Merge" version="0.6.1">
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2 <description> HUMAnN2 generated gene and pathway abundance tables</description>
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4 <macros>
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5 <import>humann2_macros.xml</import>
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6 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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11 <version_command>
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12 <![CDATA[
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13 humann2_merge_abundance_tables --version
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14 ]]>
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15 </version_command>
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17 <command><![CDATA[
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18 humann2_merge_abundance_tables
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20 --input-genes $input_gene
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21 --input-pathways $input_pathway
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23 #if $gene_mapping_selection.gene_mapping_selection_test == "true":
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24 --gene-mapping $gene_mapping
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25 #end if
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27 #if $pathway_mapping_selection.pathway_mapping_selection_test == "true":
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28 --pathway-mapping $pathway-mapping
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29 #end if
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31 $remove_taxonomy
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32
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33 -o $output_table
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34 ]]></command>
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36 <inputs>
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37 <param name="input_gene" type="data" format="tsv" label="Gene family or EC abundance file" help="(--input-genes)"/>
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38
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39 <param name="input_pathway" type="data" format="tsv" label="Pathway abundance file" help="(--input-pathways)"/>
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40
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41 <conditional name="gene_mapping_selection">
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42 <param name='gene_mapping_selection_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a gene mapping file?" help=""/>
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43 <when value="true">
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44 <param name="gene_mapping" type="data" format="tsv" label="Gene family to reaction mapping file" help="(--gene-mapping)"/>
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45 </when>
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46 <when value="false">
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47 </when>
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48 </conditional>
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49 <conditional name="pathway_mapping_selection">
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50 <param name='pathway_mapping_selection_test' type='boolean' checked="false" truevalue='true' falsevalue='false' label="Use a pathway mapping file?" help=""/>
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51 <when value="true">
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52 <param name="pathway_mapping" type="data" format="tsv" label="Reaction to pathway mapping file" help="(--pathway-mapping)"/>
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53 </when>
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54 <when value="false">
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55 </when>
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56 </conditional>
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57
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58 <param name='remove_taxonomy' type='boolean' checked="false" truevalue='--remove-taxonomy' falsevalue='' label="Remove the taxonomy from the output file?" help="(--remove-taxonomy)"/>
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59 </inputs>
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60
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61 <outputs>
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62 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Merged table" />
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="input_gene" value="expected_gene_family_abundance.tsv"/>
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68 <param name="input_pathway" value="expected_pathway_abundance.tsv"/>
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69 <param name="gene_mapping_selection_test" value="false"/>
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70 <param name="pathway_mapping_selection" value="false"/>
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71 <param name="remove_taxonomy" value="false"/>
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72 <output name="output_table" file="merged_gene_families_pathways_abundances.tsv" />
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73 </test>
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74 </tests>
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75
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76 <help><![CDATA[
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77 **What it does**
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78
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79 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
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80
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81 The currest tool merge a table containing gene family abundances with a table containing pathway abundances, given a gene to pathway mapping (default or custom one).
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82
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83 ]]></help>
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84
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85 <expand macro="citations"/>
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86 </tool>