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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit 9fcfd73aaf19aa65e2087ae003998f21971b6f9b-dirty
author bebatut
date Wed, 20 Apr 2016 09:15:07 -0400
parents 22e031055f18
children
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1:22e031055f18 2:9c24aa6d9a1f
1 <tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0"> 1 <tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0">
2 <description>and extract information</description> 2 <description>and extract similar and specific information</description>
3 3
4 <requirements> 4 <requirements>
5 </requirements> 5 </requirements>
6 6
7 <stdio> 7 <stdio>
52 </outputs> 52 </outputs>
53 53
54 <tests> 54 <tests>
55 <test> 55 <test>
56 <param name="samples_0|sample_name" value="sample1"/> 56 <param name="samples_0|sample_name" value="sample1"/>
57 <param name="samples_0|input" value="humann2_m8_pathabundance_cmp_renormalized.tsv"/> 57 <param name="samples_0|input" value="sample_1_pathway_abundances.tabular"/>
58 <param name="samples_1|sample_name" value="sample2"/> 58 <param name="samples_1|sample_name" value="sample2"/>
59 <param name="samples_1|input" value="humann2_fasta_pathabundance_relab_renormalized.csv"/> 59 <param name="samples_1|input" value="sample_2_pathway_abundances.tabular"/>
60 <param name="charact_nb" value="10"/> 60 <param name="charact_nb" value="10"/>
61 <output name="more_abundant_output_file" file="more_abundant_output.tabular"/> 61 <output name="more_abundant_output_file" file="more_abundant_pathways.tabular"/>
62 <output name="similar_output_file" file="similar_output.tabular"/> 62 <output name="similar_output_file" file="sample_similar_pathways.tabular"/>
63 <output name="log" file="log_output.txt"/> 63 <output name="log" file="sample_comparison_log.txt"/>
64 <output_collection name="specific_files" type="list"> 64 <output_collection name="specific_files" type="list">
65 <element name="specific_to_sample1" file="specific_to_sample1_output.txt" /> 65 <element name="specific_to_sample1" file="sample_1_specific_pathways.txt" />
66 <element name="specific_to_sample2" file="specific_to_sample2_output.txt" /> 66 <element name="specific_to_sample2" file="sample_2_specific_pathways.txt" />
67 </output_collection> 67 </output_collection>
68 </test> 68 </test>
69 </tests> 69 </tests>
70 70
71 <help><![CDATA[ 71 <help><![CDATA[
74 This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted: 74 This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted:
75 75
76 * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics 76 * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics
77 77
78 * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples 78 * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
79 79
80 * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics 80 * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics
81 81
82 ]]></help> 82 ]]></help>
83 83
84 <citations> 84 <citations>