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annotate humann2_renorm_table.xml @ 9:7d2be77d5b83 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
author bebatut
date Thu, 31 Mar 2016 03:35:17 -0400
parents 0d3d44f13122
children e504cd2410a6
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1 <tool id="humann2_renorm_table" name="Renormalize HUMAnN2 table" version="0.5.0">
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2 <description></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_renorm_table --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_renorm_table
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19 -i $input_table
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20 -o $output_table
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21 --norm $norm
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22 ]]></command>
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24 <inputs>
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25 <param name="input_table" type="data" format="tsv" label="Gene/pathway
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26 table" help=""/>
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28 <param name="norm" type="select" label="Normalization scheme" help="(--norm)">
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29 <option value="cpm" selected="true">Copies per million</option>
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30 <option value="relab">Relative abundance</option>
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31 </param>
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32 </inputs>
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34 <outputs>
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35 <data format="tsv" name="output_table" label="Normalized table for
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36 ${on_string} (HUMAnN2)" />
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37 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
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42 <param name="norm" value="cpm"/>
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43 <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/>
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44 </test>
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45 <test>
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46 <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
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47 <param name="norm" value="relab"/>
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48 <output name="output_table" file="humann2_fasta_pathabundance_relab_renormalized.tsv"/>
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49 </test>
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50 </tests>
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52 <help><![CDATA[
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53 **What it does**
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55 Renorm HUMAnN2 table is a tool for renormalizing table. Each level of a stratified table will be normalized using the desired scheme.
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57 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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59 ]]></help>
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61 <citations>
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62 </citations>
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63 </tool>