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comparison compare_humann2_output.xml @ 0:035a848cb73e draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 02:56:13 -0400
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1 <tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0">
2 <description>and extract information</description>
3
4 <requirements>
5 </requirements>
6
7 <stdio>
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 </stdio>
11
12 <version_command></version_command>
13
14 <command><![CDATA[
15 mkdir specifics
16 &&
17
18 python $__tool_directory__/compare_humann2_output.py
19 #for $sample in $samples:
20 --sample_name "${sample.sample_name}"
21 --charact_input_file "${sample.input}"
22 --specific_output_file "specifics/specific_to_${sample.sample_name}.txt"
23 #end for
24
25 --most_abundant_characteristics_to_extract $charact_nb
26 --more_abundant_output_file $more_abundant_output_file
27 --similar_output_file $similar_output_file
28 > $log
29
30 ]]></command>
31
32 <inputs>
33 <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" >
34 <param name="sample_name" type="text" label="Name of the sample" help="(--sample_name)"/>
35 <param name="input" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization, --charact_input_file)"/>
36 </repeat>
37
38 <param name="charact_nb" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample" help="(--most_abundant_characteristics_to_extract)"/>
39 </inputs>
40
41 <outputs>
42 <data name="more_abundant_output_file" format="tabular"
43 label="${tool.name} on ${on_string}: More abundant characteristics for each sample" />
44 <data name="similar_output_file" format="tabular"
45 label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" />
46 <data name="log" format="txt"
47 label="${tool.name} on ${on_string}: Log" />
48 <collection name="specific_files" type="list">
49 <discover_datasets pattern="__designation_and_ext__" directory="specifics"/>
50 </collection>
51
52 </outputs>
53
54 <tests>
55 </tests>
56
57 <help><![CDATA[
58 **What it does**
59
60 This tool compare HUMANnN2 outputs with gene families or pathways relative abundances of several samples and extract several files:
61
62 - Similar gene families or pathways between the samples and the relative abundances and these similar characteristics
63 - Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
64
65 ]]></help>
66
67 <citations>
68 </citations>
69 </tool>