Mercurial > repos > bebatut > compare_humann2_output

annotate 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
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05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
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1 <tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.2.0">
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2 <description>and extract similar and specific information</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 mkdir specifics
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5 &&
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7 python $__tool_directory__/compare_humann2_output.py
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8 #for $sample in $samples
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9 --sample_name '$sample.sample_name'
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10 --charact_input_fp '$sample.charact_input_fp'
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11 --specific_output_fp 'specifics/specific_to_${sample.sample_name}.txt'
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12 #end for
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13 --most_abundant_characteristics_to_extract $most_abundant_characteristics_to_extract
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14 --more_abundant_output_fp '$more_abundant_output_file'
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15 --similar_output_fp '$similar_output_file'
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16 > $log
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17 ]]></command>
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18 <inputs>
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19 <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" >
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20 <param argument="sample_name" type="text" label="Name of the sample"/>
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21 <param argument="charact_input_fp" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization"/>
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22 </repeat>
2
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23 <param argument="most_abundant_characteristics_to_extract" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample"/>
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24 </inputs>
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25 <outputs>
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26 <data name="more_abundant_output_file" format="tabular"
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27 label="${tool.name} on ${on_string}: More abundant characteristics for each sample" />
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28 <data name="similar_output_file" format="tabular"
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29 label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" />
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30 <data name="log" format="txt"
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31 label="${tool.name} on ${on_string}: Log" hidden="true"/>
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32 <collection name="specific_files" type="list">
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33 <discover_datasets pattern="__designation_and_ext__" directory="specifics"/>
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34 </collection>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <repeat name="samples">
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39 <param name="sample_name" value="sample1"/>
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40 <param name="charact_input_fp" value="sample_1_pathway_abundances.tabular"/>
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41 </repeat>
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42 <repeat name="samples">
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43 <param name="sample_name" value="sample2"/>
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44 <param name="charact_input_fp" value="sample_2_pathway_abundances.tabular"/>
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45 </repeat>
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46 <param name="most_abundant_characteristics_to_extract" value="10"/>
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47 <output name="more_abundant_output_file">
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48 <assert_contents>
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49 <has_n_columns n="4"/>
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50 <has_n_lines n="16"/>
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51 <has_text text="aerobic respiration I |g__Rhodobacter.s__Rhodobacter_sphaeroides"/>
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52 <has_text text="phytol degradation|g__Staphylococcus.s__Staphylococcus_aureus"/>
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53 </assert_contents>
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54 </output>
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55 <output name="similar_output_file">
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56 <assert_contents>
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57 <has_n_columns n="4"/>
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58 <has_n_lines n="1921"/>
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59 <has_text text="superpathway of sulfur amino acid biosynthesis |g__Staphylococcus.s__Staphylococcus_epidermidis"/>
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60 <has_text text="tetrapyrrole biosynthesis I |g__Pseudomonas.s__Pseudomonas_aeruginosa"/>
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61 </assert_contents>
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62 </output>
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63 <output name="log">
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64 <assert_contents>
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65 <has_n_lines n="12"/>
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66 <has_line line="Similar between all samples: 1920"/>
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67 <has_line line=" Number of specific characteristics: 392"/>
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68 <has_line line=" Number of specific characteristics: 1335"/>
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69 </assert_contents>
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70 </output>
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71 <output_collection name="specific_files" type="list">
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72 <element name="specific_to_sample1">
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73 <assert_contents>
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74 <has_n_columns n="3"/>
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75 <has_n_lines n="393"/>
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76 <has_text text="GLUCOSE1PMETAB-PWY"/>
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77 <has_text text="inosine 5 phosphate biosynthesis III|g__Staphylococcus.s__Staphylococcus_aureus"/>
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78 </assert_contents>
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79 </element>
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80 <element name="specific_to_sample2">
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81 <assert_contents>
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
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82 <has_n_columns n="3"/>
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
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83 <has_n_lines n="1336"/>
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
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84 <has_text text="PEPTIDOGLYCANSYN-PWY"/>
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
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85 <has_text text="nitrate reduction V |g__Deinococcus.s__Deinococcus_radiodurans"/>
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
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86 </assert_contents>
05766022dfc4 "planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit dc55dc3b5275d1d6aac390698c0c6e0ab8fbf2f7"
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87 </element>
0
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88 </output_collection>
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89 </test>
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90 </tests>
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91 <help><![CDATA[
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92 **What it does**
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93
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94 This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted:
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95
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96 * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics
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97
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98 * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
1
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99
0
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100 * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics
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101
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102 ]]></help>
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103 </tool>