Mercurial > repos > iuc > picrust_categorize

comparison categorize_by_function.xml @ 0:a94f4d96045c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
author iuc
date Thu, 08 Dec 2016 06:27:47 -0500
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-1:000000000000 0:a94f4d96045c
1 <tool id="picrust_categorize" name="Categorize by function" version="@WRAPPER_VERSION@.0">
2 <description>collapse hierarchical data to a specified level</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 categorize_by_function.py
10 -i '$input_fp'
11 -c $metadata_category
12 -l $level
13 -o tempbiom
14 $format_tab_delimited
15
16 @OUTPUT_CONVERSION_COMMANDS@
17 ]]></command>
18 <inputs>
19 <param argument="--input_fp" format="tabular,biom1" type="data" label="Input file" help="the output from the PICRISt predict tool"/>
20 <param argument="--metadata_category" type="select" multiple="false" label="Metadata category that describes the hierarchy" help="">
21 <option value="KEGG_Pathways" selected="true">KEGG Pathways</option>
22 <option value="COG_Category">COG Category</option>
23 <option value="taxonomy">Using taxonomy metadata</option>
24 </param>
25 <param argument="--level" type="integer" value="3" min="1" label="Hierarchy Level"
26 help="a value of 1 is the highest level, and any higher value nears the leaves of the hierarchy. For instance, if the hierarchy contains 4 levels, specifying 3 would collapse at one level above being fully specified"/>
27 <param argument="--format_tab_delimited" type="boolean" truevalue="-f" falsevalue="" checked="false" label="output the predicted metagenome table in tab-delimited" help="will contain the metadata lost in the classic output"/>
28 <expand macro="biom_format_select"/>
29 </inputs>
30 <outputs>
31 <expand macro="biom_output"/>
32 <data name="out_tabdel" format="tabular" from_work_dir="tempbiom" label="${tool.name} on ${on_string}: metagenome table">
33 <filter>format_tab_delimited</filter>
34 </data>
35 </outputs>
36 <tests>
37 <test> <!-- test with Kegg Pathways and json output -->
38 <param name="input_fp" value="predicted_metagenomes.L3.biom"/>
39 <param name="metadata_category" value="KEGG_Pathways"/>
40 <param name="level" value="2"/>
41 <param name="format_tab_delimited" value="-f"/>
42 <param name="output_type" value="json"/>
43 <output name="out_biom" ftype="json">
44 <assert_contents>
45 <has_text text="Biological Observation Matrix"/>
46 <has_text text="generated_by"/>
47 <has_text text="KEGG_Pathways"/>
48 <has_text text="Cancers"/>
49 <not_has_text text="ABC transporters"/>
50 </assert_contents>
51 </output>
52 <output name="out_tabdel" ftype="tabular" file="tempout.table"/>
53 </test>
54 <test> <!-- test with COG categories and classic output -->
55 <param name="input_fp" value="cog_predicted_metagenomes.L2.biom"/>
56 <param name="metadata_category" value="COG_Category"/>
57 <param name="level" value="1"/>
58 <param name="format_tab_delimited" value="-f"/>
59 <param name="output_type" value="tsv"/>
60 <output name="out_biom" ftype="tabular" md5="7682875d365f884b399ffa521952dbd8"/>
61 <output name="out_tabdel" ftype="tabular" md5="e3545484ff53bf8650725573af2ebbb9"/>
62 </test>
63 <test> <!-- test with taxonomy metadata and hdf5 output -->
64 <param name="input_fp" value="observation_table.biom"/>
65 <param name="metadata_category" value="taxonomy"/>
66 <param name="level" value="1"/>
67 <param name="output_type" value="hdf5"/>
68 <output name="out_biom" ftype="hdf5" file="categorize_biom.hdf5" compare="sim_size"/>
69 </test>
70 </tests>
71 <help>
72 <![CDATA[
73 @PICRUST_OVERVIEW@
74
75 **Command Documentation**
76
77 This module collapses hierarchical data to a specified level for PICRUSt predictions. For instance, often it is useful to examine KEGG results from a higher level within the pathway hierarchy.
78 Many genes are sometimes involved in multiple pathways, and in these circumstances (also know as a one-to-many relationship), the gene is counted for each pathway.
79
80 **Input file:** Output file from the predict tool
81
82 ]]>
83 </help>
84 <expand macro="citations"/>
85 </tool>