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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
author bebatut
date Wed, 20 Apr 2016 08:30:08 -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 <test>
56 <param name="samples_0|sample_name" value="sample1"/>
57 <param name="samples_0|input" value="humann2_m8_pathabundance_cmp_renormalized.tsv"/>
58 <param name="samples_1|sample_name" value="sample2"/>
59 <param name="samples_1|input" value="humann2_fasta_pathabundance_relab_renormalized.csv"/>
60 <param name="charact_nb" value="10"/>
61 <output name="more_abundant_output_file" file="more_abundant_output.tabular"/>
62 <output name="similar_output_file" file="similar_output.tabular"/>
63 <output name="log" file="log_output.txt"/>
64 <output_collection name="specific_files" type="list">
65 <element name="specific_to_sample1" file="specific_to_sample1_output.txt" />
66 <element name="specific_to_sample2" file="specific_to_sample2_output.txt" />
67 </output_collection>
68 </test>
69 </tests>
70
71 <help><![CDATA[
72 **What it does**
73
74 This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted:
75
76 * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics
77
78 * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
79
80 * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics
81
82 ]]></help>
83
84 <citations>
85 </citations>
86 </tool>