Mercurial > repos > iuc > humann2_renorm_table

annotate humann2_renorm_table.xml @ 1:dbf0e8eeeeed draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:55:54 -0400
parents ba4dfbdc1295
children cd235981c423
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ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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1 <tool id="humann2_renorm_table" name="Renormalize" version="@WRAPPER_VERSION@.0">
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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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>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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6 <expand macro="requirements"/>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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7 <expand macro="version"/>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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8 <command detect_errors="exit_code"><![CDATA[
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dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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9 humann2_renorm_table
dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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10 --input '$input'
dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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11 -o '$output_table'
dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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12 --units '$units'
dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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13 --mode '$mode'
dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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14 --special '$special'
dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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15 $update_snames
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16 ]]></command>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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17 <inputs>
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18 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
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19 <param argument="--units" type="select" label="Normalization scheme">
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20 <option value="cpm" selected="true">Copies per million</option>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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21 <option value="relab">Relative abundance</option>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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22 </param>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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23 <param argument="--mode" type="select" label="Normalization level">
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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24 <option value="community" selected="true">Normalization of all levels by community total</option>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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25 <option value="levelwise">Normalization of all levels by levelwise total</option>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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26 </param>
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27 <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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28 <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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ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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29 </inputs>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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30 <outputs>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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31 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" />
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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32 </outputs>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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33 <tests>
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34 <test>
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35 <param name="input" value="demo_pathabundance.tsv"/>
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36 <param name="units" value="cpm"/>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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37 <param name="mode" value="community"/>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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38 <param name="special" value="n"/>
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dbf0e8eeeeed planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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39 <param name="update_snames" value=""/>
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40 <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/>
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41 </test>
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42 <test>
ba4dfbdc1295 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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43 <param name="input" value="demo_pathabundance.tsv"/>
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44 <param name="units" value="relab"/>
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45 <param name="mode" value="levelwise"/>
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46 <param name="special" value="y"/>
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47 <param name="update_snames" value=""/>
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48 <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 @HELP_HEADER@
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53
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54 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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55
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56 ]]></help>
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57 <expand macro="citations"/>
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58 </tool>