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annotate in_development/humann2_merge_abundance_tables.xml @ 4:c05e34aa939b draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit e5b8f29dde45dddcda6ee283212dd1bdde487f87-dirty
author bebatut
date Fri, 18 Dec 2015 05:05:04 -0500
parents 947012405a6e
children 0d3d44f13122
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947012405a6e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
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1 <tool id="humann2_merge_abundance_tables" name="Merge HUMAnN2 gene and pathway abundance tables" version="0.1.0">
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2 <description></description>
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4 <requirements>
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5 <requirement type="package" version="2.2.4">bowtie2</requirement>
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6 <requirement type="package" version="2.0">metaphlan2</requirement>
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7 <requirement type="package" version="0.6.13">diamond</requirement>
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8 <requirement type="package" version="2.0">humann2</requirement>
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9 </requirements>
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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15 <version_command>
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16 <![CDATA[
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17 humann2_merge_abundance_tables --version
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18 ]]>
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19 </version_command>
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21 <command><![CDATA[
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22 humann2_merge_abundance_tables
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23 --input-genes $input_gene
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24 --input-pathways $input_pathway
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25 --gene-mapping $gene_mapping
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26 --pathway-mapping $pathway-mapping
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27 $remove_taxonomy
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28
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29 -o $output_table
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30 ]]></command>
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31
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32 <inputs>
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33 <param name="input_gene" type="data" format="tsv" label="Gene family or EC
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34 abundance file" help="(--input-genes)"/>
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35 <param name="input_pathway" type="data" format="tsv" label="Pathway
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36 abundance file" help="(--input-pathways)"/>
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37 <param name="gene_mapping" type="data" format="tsv" label="Gene family
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38 to reaction mapping file" help="(--gene-mapping)"/>
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39 <param name="pathway_mapping" type="data" format="tsv" label="Reaction to
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40 pathway mapping file" help="(--pathway-mapping)"/>
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41 <param name='remove_taxonomy' type='boolean' checked="false"
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42 truevalue='--remove-taxonomy' falsevalue=''
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43 label="Remove the taxonomy from the output file?"
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44 help="(--remove-taxonomy)"/>
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46 </inputs>
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47
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48 <outputs>
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49 <data format="tsv" name="output_table" label="Merged table for
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50 ${on_string} (HUMAnN2)" />
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51 </outputs>
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52
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53 <tests>
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54 </tests>
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56 <help><![CDATA[
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57 **What it does**
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58
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59 This tool merge gene and pathway abundance tables.
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60
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61 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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62
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63 ]]></help>
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64
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65 <citations>
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66 </citations>
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67 </tool>