Mercurial > repos > iuc > humann2_renorm_table
comparison humann2_renorm_table.xml @ 1:dbf0e8eeeeed draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author | iuc |
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date | Tue, 01 Aug 2017 07:55:54 -0400 |
parents | ba4dfbdc1295 |
children | cd235981c423 |
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0:ba4dfbdc1295 | 1:dbf0e8eeeeed |
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4 <import>humann2_macros.xml</import> | 4 <import>humann2_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="version"/> | 7 <expand macro="version"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 humann2_renorm_table | 9 humann2_renorm_table |
10 --input '$input' | 10 --input '$input' |
11 -o '$output_table' | 11 -o '$output_table' |
12 --units '$units' | 12 --units '$units' |
13 --mode '$mode' | 13 --mode '$mode' |
14 --special '$special' | 14 --special '$special' |
15 $update_snames | |
15 ]]></command> | 16 ]]></command> |
16 <inputs> | 17 <inputs> |
17 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> | 18 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> |
18 <param argument="--units" type="select" label="Normalization scheme"> | 19 <param argument="--units" type="select" label="Normalization scheme"> |
19 <option value="cpm" selected="true">Copies per million</option> | 20 <option value="cpm" selected="true">Copies per million</option> |
21 </param> | 22 </param> |
22 <param argument="--mode" type="select" label="Normalization level"> | 23 <param argument="--mode" type="select" label="Normalization level"> |
23 <option value="community" selected="true">Normalization of all levels by community total</option> | 24 <option value="community" selected="true">Normalization of all levels by community total</option> |
24 <option value="levelwise">Normalization of all levels by levelwise total</option> | 25 <option value="levelwise">Normalization of all levels by levelwise total</option> |
25 </param> | 26 </param> |
26 <param argument="--special" type='boolean' checked="true" truevalue='y' falsevalue='n' label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/> | 27 <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/> |
28 <param name="update_snames" argument="--update-snames" type='boolean' truevalue='--update-snames' falsevalue='' checked="true" label="Update '-RPK' in sample names to appropriate suffix?"/> | |
27 </inputs> | 29 </inputs> |
28 <outputs> | 30 <outputs> |
29 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" /> | 31 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" /> |
30 </outputs> | 32 </outputs> |
31 <tests> | 33 <tests> |
32 <test> | 34 <test> |
33 <param name="input" value="demo_pathabundance.tsv"/> | 35 <param name="input" value="demo_pathabundance.tsv"/> |
34 <param name="units" value="cpm"/> | 36 <param name="units" value="cpm"/> |
35 <param name="mode" value="community"/> | 37 <param name="mode" value="community"/> |
36 <param name="special" value="n"/> | 38 <param name="special" value="n"/> |
39 <param name="update_snames" value=""/> | |
37 <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/> | 40 <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/> |
38 </test> | 41 </test> |
39 <test> | 42 <test> |
40 <param name="input" value="demo_pathabundance.tsv"/> | 43 <param name="input" value="demo_pathabundance.tsv"/> |
41 <param name="units" value="relab"/> | 44 <param name="units" value="relab"/> |
42 <param name="mode" value="levelwise"/> | 45 <param name="mode" value="levelwise"/> |
43 <param name="special" value="y"/> | 46 <param name="special" value="y"/> |
47 <param name="update_snames" value=""/> | |
44 <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/> | 48 <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/> |
45 </test> | 49 </test> |
46 </tests> | 50 </tests> |
47 <help><![CDATA[ | 51 <help><![CDATA[ |
48 @HELP_HEADER@ | 52 @HELP_HEADER@ |