annotate humann2_renorm_table.xml @ 6:c6676a890f50 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 06:59:13 +0000
parents cd235981c423
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cd235981c423 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
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1 <tool id="humann2_renorm_table" name="Renormalize" version="@WRAPPER_VERSION@.1">
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2 <description>a HUMAnN2 generated table</description>
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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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cd235981c423 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
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6 <expand macro="stdio"/>
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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[
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10 humann2_renorm_table
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11 --input '$input'
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12 -o '$output_table'
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13 --units '$units'
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14 --mode '$mode'
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15 --special '$special'
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16 $update_snames
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17 ]]></command>
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18 <inputs>
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19 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
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20 <param argument="--units" type="select" label="Normalization scheme">
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21 <option value="cpm" selected="true">Copies per million</option>
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22 <option value="relab">Relative abundance</option>
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23 </param>
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24 <param argument="--mode" type="select" label="Normalization level">
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25 <option value="community" selected="true">Normalization of all levels by community total</option>
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26 <option value="levelwise">Normalization of all levels by levelwise total</option>
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27 </param>
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28 <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
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29 <param name="update_snames" argument="--update-snames" type='boolean' truevalue='--update-snames' falsevalue='' checked="true" label="Update '-RPK' in sample names to appropriate suffix?"/>
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30 </inputs>
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31 <outputs>
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32 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="demo_pathabundance.tsv"/>
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37 <param name="units" value="cpm"/>
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38 <param name="mode" value="community"/>
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39 <param name="special" value="n"/>
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40 <param name="update_snames" value=""/>
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41 <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/>
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42 </test>
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43 <test>
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44 <param name="input" value="demo_pathabundance.tsv"/>
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45 <param name="units" value="relab"/>
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46 <param name="mode" value="levelwise"/>
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47 <param name="special" value="y"/>
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48 <param name="update_snames" value=""/>
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49 <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53 @HELP_HEADER@
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54
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55 Renorm HUMAnN2 table is a tool to renormalize a table, either in copies per million or in relative abundance. Each level of a stratified table will be normalized using the desired scheme.
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56
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57 ]]></help>
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58 <expand macro="citations"/>
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59 </tool>