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comparison compare_humann2_output.xml @ 2:05766022dfc4 draft

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"planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
author bebatut
date Mon, 14 Sep 2020 13:50:30 +0000
parents c1aca37cb1fc
children 844fcd42ec7c
comparison
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1:c1aca37cb1fc 2:05766022dfc4
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="0.2.0">
2 <description>and extract similar and specific information</description> 2 <description>and extract similar and specific information</description>
3 3 <command detect_errors="exit_code"><![CDATA[
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 4 mkdir specifics
16 && 5 &&
17 6
18 python $__tool_directory__/compare_humann2_output.py 7 python $__tool_directory__/compare_humann2_output.py
19 #for $sample in $samples: 8 #for $sample in $samples
20 --sample_name "${sample.sample_name}" 9 --sample_name '$sample.sample_name'
21 --charact_input_file "${sample.input}" 10 --charact_input_fp '$sample.charact_input_fp'
22 --specific_output_file "specifics/specific_to_${sample.sample_name}.txt" 11 --specific_output_fp 'specifics/specific_to_${sample.sample_name}.txt'
23 #end for 12 #end for
24 13 --most_abundant_characteristics_to_extract $most_abundant_characteristics_to_extract
25 --most_abundant_characteristics_to_extract $charact_nb 14 --more_abundant_output_fp '$more_abundant_output_file'
26 --more_abundant_output_file $more_abundant_output_file 15 --similar_output_fp '$similar_output_file'
27 --similar_output_file $similar_output_file
28 > $log 16 > $log
29
30 ]]></command> 17 ]]></command>
31
32 <inputs> 18 <inputs>
33 <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" > 19 <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" >
34 <param name="sample_name" type="text" label="Name of the sample" help="(--sample_name)"/> 20 <param argument="sample_name" type="text" label="Name of the sample"/>
35 <param name="input" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization, --charact_input_file)"/> 21 <param argument="charact_input_fp" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization"/>
36 </repeat> 22 </repeat>
37 23 <param argument="most_abundant_characteristics_to_extract" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample"/>
38 <param name="charact_nb" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample" help="(--most_abundant_characteristics_to_extract)"/>
39 </inputs> 24 </inputs>
40
41 <outputs> 25 <outputs>
42 <data name="more_abundant_output_file" format="tabular" 26 <data name="more_abundant_output_file" format="tabular"
43 label="${tool.name} on ${on_string}: More abundant characteristics for each sample" /> 27 label="${tool.name} on ${on_string}: More abundant characteristics for each sample" />
44 <data name="similar_output_file" format="tabular" 28 <data name="similar_output_file" format="tabular"
45 label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" /> 29 label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" />
46 <data name="log" format="txt" 30 <data name="log" format="txt"
47 label="${tool.name} on ${on_string}: Log" /> 31 label="${tool.name} on ${on_string}: Log" hidden="true"/>
48 <collection name="specific_files" type="list"> 32 <collection name="specific_files" type="list">
49 <discover_datasets pattern="__designation_and_ext__" directory="specifics"/> 33 <discover_datasets pattern="__designation_and_ext__" directory="specifics"/>
50 </collection> 34 </collection>
51
52 </outputs> 35 </outputs>
53
54 <tests> 36 <tests>
55 <test> 37 <test>
56 <param name="samples_0|sample_name" value="sample1"/> 38 <repeat name="samples">
57 <param name="samples_0|input" value="sample_1_pathway_abundances.tabular"/> 39 <param name="sample_name" value="sample1"/>
58 <param name="samples_1|sample_name" value="sample2"/> 40 <param name="charact_input_fp" value="sample_1_pathway_abundances.tabular"/>
59 <param name="samples_1|input" value="sample_2_pathway_abundances.tabular"/> 41 </repeat>
60 <param name="charact_nb" value="10"/> 42 <repeat name="samples">
61 <output name="more_abundant_output_file" file="more_abundant_pathways.tabular"/> 43 <param name="sample_name" value="sample2"/>
62 <output name="similar_output_file" file="sample_similar_pathways.tabular"/> 44 <param name="charact_input_fp" value="sample_2_pathway_abundances.tabular"/>
63 <output name="log" file="sample_comparison_log.txt"/> 45 </repeat>
46 <param name="most_abundant_characteristics_to_extract" value="10"/>
47 <output name="more_abundant_output_file">
48 <assert_contents>
49 <has_n_columns n="4"/>
50 <has_n_lines n="16"/>
51 <has_text text="aerobic respiration I |g__Rhodobacter.s__Rhodobacter_sphaeroides"/>
52 <has_text text="phytol degradation|g__Staphylococcus.s__Staphylococcus_aureus"/>
53 </assert_contents>
54 </output>
55 <output name="similar_output_file">
56 <assert_contents>
57 <has_n_columns n="4"/>
58 <has_n_lines n="1921"/>
59 <has_text text="superpathway of sulfur amino acid biosynthesis |g__Staphylococcus.s__Staphylococcus_epidermidis"/>
60 <has_text text="tetrapyrrole biosynthesis I |g__Pseudomonas.s__Pseudomonas_aeruginosa"/>
61 </assert_contents>
62 </output>
63 <output name="log">
64 <assert_contents>
65 <has_n_lines n="12"/>
66 <has_line line="Similar between all samples: 1920"/>
67 <has_line line=" Number of specific characteristics: 392"/>
68 <has_line line=" Number of specific characteristics: 1335"/>
69 </assert_contents>
70 </output>
64 <output_collection name="specific_files" type="list"> 71 <output_collection name="specific_files" type="list">
65 <element name="specific_to_sample1" file="sample_1_specific_pathways.txt" /> 72 <element name="specific_to_sample1">
66 <element name="specific_to_sample2" file="sample_2_specific_pathways.txt" /> 73 <assert_contents>
74 <has_n_columns n="3"/>
75 <has_n_lines n="393"/>
76 <has_text text="GLUCOSE1PMETAB-PWY"/>
77 <has_text text="inosine 5 phosphate biosynthesis III|g__Staphylococcus.s__Staphylococcus_aureus"/>
78 </assert_contents>
79 </element>
80 <element name="specific_to_sample2">
81 <assert_contents>
82 <has_n_columns n="3"/>
83 <has_n_lines n="1336"/>
84 <has_text text="PEPTIDOGLYCANSYN-PWY"/>
85 <has_text text="nitrate reduction V |g__Deinococcus.s__Deinococcus_radiodurans"/>
86 </assert_contents>
87 </element>
67 </output_collection> 88 </output_collection>
68 </test> 89 </test>
69 </tests> 90 </tests>
70
71 <help><![CDATA[ 91 <help><![CDATA[
72 **What it does** 92 **What it does**
73 93
74 This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted: 94 This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted:
75 95
78 * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples 98 * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
79 99
80 * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics 100 * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics
81 101
82 ]]></help> 102 ]]></help>
83
84 <citations>
85 </citations>
86 </tool> 103 </tool>