Mercurial > repos > iuc > picrust_categorize

comparison categorize_by_function.xml @ 1:fd5533e57354 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
author iuc
date Wed, 30 Aug 2017 04:49:00 -0400
parents a94f4d96045c
children 36e87158ef04
comparison
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0:a94f4d96045c 1:fd5533e57354
1 <tool id="picrust_categorize" name="Categorize by function" version="@WRAPPER_VERSION@.0"> 1 <tool id="picrust_categorize" name="Categorize" version="@WRAPPER_VERSION@.0">
2 <description>collapse hierarchical data to a specified level</description> 2 <description>by collapsing hierarchical data to a specified functional level</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_command"/> 7 <expand macro="version_command"/>
9 categorize_by_function.py 9 categorize_by_function.py
10 -i '$input_fp' 10 -i '$input_fp'
11 -c $metadata_category 11 -c $metadata_category
12 -l $level 12 -l $level
13 -o tempbiom 13 -o tempbiom
14 $format_tab_delimited
15 14
16 @OUTPUT_CONVERSION_COMMANDS@ 15 @OUTPUT_CONVERSION_COMMANDS@
17 ]]></command> 16 ]]></command>
18 <inputs> 17 <inputs>
19 <param argument="--input_fp" format="tabular,biom1" type="data" label="Input file" help="the output from the PICRISt predict tool"/> 18 <param argument="--input_fp" format="biom1,h5" type="data" label="Input file" help="Biom file that is output from the PICRISt predict tool"/>
20 <param argument="--metadata_category" type="select" multiple="false" label="Metadata category that describes the hierarchy" help=""> 19 <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> 20 <option value="KEGG_Pathways" selected="true">KEGG Pathways</option>
22 <option value="COG_Category">COG Category</option> 21 <option value="COG_Category">COG Category</option>
23 <option value="taxonomy">Using taxonomy metadata</option> 22 <option value="taxonomy">Using taxonomy metadata</option>
24 </param> 23 </param>
25 <param argument="--level" type="integer" value="3" min="1" label="Hierarchy Level" 24 <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"/> 25 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"/> 26 <expand macro="biom_format_select"/>
29 </inputs> 27 </inputs>
30 <outputs> 28 <outputs>
31 <expand macro="biom_output"/> 29 <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> 30 </outputs>
36 <tests> 31 <tests>
37 <test> <!-- test with Kegg Pathways and json output --> 32 <test> <!-- test with Kegg Pathways and json output -->
38 <param name="input_fp" value="predicted_metagenomes.L3.biom"/> 33 <param name="input_fp" value="predicted_metagenomes.L3.biom"/>
39 <param name="metadata_category" value="KEGG_Pathways"/> 34 <param name="metadata_category" value="KEGG_Pathways"/>
40 <param name="level" value="2"/> 35 <param name="level" value="2"/>
41 <param name="format_tab_delimited" value="-f"/>
42 <param name="output_type" value="json"/> 36 <param name="output_type" value="json"/>
43 <output name="out_biom" ftype="json"> 37 <output name="out_biom" ftype="biom1">
44 <assert_contents> 38 <assert_contents>
45 <has_text text="Biological Observation Matrix"/> 39 <has_text text="Biological Observation Matrix"/>
46 <has_text text="generated_by"/> 40 <has_text text="generated_by"/>
47 <has_text text="KEGG_Pathways"/> 41 <has_text text="KEGG_Pathways"/>
48 <has_text text="Cancers"/> 42 <has_text text="Cancers"/>
49 <not_has_text text="ABC transporters"/> 43 <not_has_text text="ABC transporters"/>
50 </assert_contents> 44 </assert_contents>
51 </output> 45 </output>
52 <output name="out_tabdel" ftype="tabular" file="tempout.table"/>
53 </test> 46 </test>
54 <test> <!-- test with COG categories and classic output --> 47 <test> <!-- test with COG categories and classic output -->
55 <param name="input_fp" value="cog_predicted_metagenomes.L2.biom"/> 48 <param name="input_fp" value="cog_predicted_metagenomes.L2.biom"/>
56 <param name="metadata_category" value="COG_Category"/> 49 <param name="metadata_category" value="COG_Category"/>
57 <param name="level" value="1"/> 50 <param name="level" value="1"/>
58 <param name="format_tab_delimited" value="-f"/>
59 <param name="output_type" value="tsv"/> 51 <param name="output_type" value="tsv"/>
60 <output name="out_biom" ftype="tabular" md5="7682875d365f884b399ffa521952dbd8"/> 52 <output name="out_biom" ftype="tabular" md5="7682875d365f884b399ffa521952dbd8"/>
61 <output name="out_tabdel" ftype="tabular" md5="e3545484ff53bf8650725573af2ebbb9"/>
62 </test> 53 </test>
63 <test> <!-- test with taxonomy metadata and hdf5 output --> 54 <test> <!-- test with taxonomy metadata and hdf5 output -->
64 <param name="input_fp" value="observation_table.biom"/> 55 <param name="input_fp" value="observation_table.biom"/>
65 <param name="metadata_category" value="taxonomy"/> 56 <param name="metadata_category" value="taxonomy"/>
66 <param name="level" value="1"/> 57 <param name="level" value="1"/>
67 <param name="output_type" value="hdf5"/> 58 <param name="output_type" value="hdf5"/>
68 <output name="out_biom" ftype="hdf5" file="categorize_biom.hdf5" compare="sim_size"/> 59 <output name="out_biom" ftype="h5" file="categorize_biom.hdf5" compare="sim_size"/>
69 </test> 60 </test>
70 </tests> 61 </tests>
71 <help> 62 <help>
72 <![CDATA[ 63 <![CDATA[
73 @PICRUST_OVERVIEW@ 64 @PICRUST_OVERVIEW@