Mercurial > repos > bebatut > compare_humann2_output
diff compare_humann2_output.xml @ 2:05766022dfc4 draft
"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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--- a/compare_humann2_output.xml Wed Apr 20 09:15:27 2016 -0400 +++ b/compare_humann2_output.xml Mon Sep 14 13:50:30 2020 +0000 @@ -1,73 +1,93 @@ -<tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0"> +<tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.2.0"> <description>and extract similar and specific information</description> - - <requirements> - </requirements> - - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - - <version_command></version_command> - - <command><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ mkdir specifics && python $__tool_directory__/compare_humann2_output.py - #for $sample in $samples: - --sample_name "${sample.sample_name}" - --charact_input_file "${sample.input}" - --specific_output_file "specifics/specific_to_${sample.sample_name}.txt" + #for $sample in $samples + --sample_name '$sample.sample_name' + --charact_input_fp '$sample.charact_input_fp' + --specific_output_fp 'specifics/specific_to_${sample.sample_name}.txt' #end for - - --most_abundant_characteristics_to_extract $charact_nb - --more_abundant_output_file $more_abundant_output_file - --similar_output_file $similar_output_file + --most_abundant_characteristics_to_extract $most_abundant_characteristics_to_extract + --more_abundant_output_fp '$more_abundant_output_file' + --similar_output_fp '$similar_output_file' > $log - ]]></command> - <inputs> <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" > - <param name="sample_name" type="text" label="Name of the sample" help="(--sample_name)"/> - <param name="input" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization, --charact_input_file)"/> + <param argument="sample_name" type="text" label="Name of the sample"/> + <param argument="charact_input_fp" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization"/> </repeat> - - <param name="charact_nb" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample" help="(--most_abundant_characteristics_to_extract)"/> + <param argument="most_abundant_characteristics_to_extract" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample"/> </inputs> - <outputs> <data name="more_abundant_output_file" format="tabular" label="${tool.name} on ${on_string}: More abundant characteristics for each sample" /> <data name="similar_output_file" format="tabular" label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" /> <data name="log" format="txt" - label="${tool.name} on ${on_string}: Log" /> + label="${tool.name} on ${on_string}: Log" hidden="true"/> <collection name="specific_files" type="list"> <discover_datasets pattern="__designation_and_ext__" directory="specifics"/> </collection> - </outputs> - <tests> <test> - <param name="samples_0|sample_name" value="sample1"/> - <param name="samples_0|input" value="sample_1_pathway_abundances.tabular"/> - <param name="samples_1|sample_name" value="sample2"/> - <param name="samples_1|input" value="sample_2_pathway_abundances.tabular"/> - <param name="charact_nb" value="10"/> - <output name="more_abundant_output_file" file="more_abundant_pathways.tabular"/> - <output name="similar_output_file" file="sample_similar_pathways.tabular"/> - <output name="log" file="sample_comparison_log.txt"/> + <repeat name="samples"> + <param name="sample_name" value="sample1"/> + <param name="charact_input_fp" value="sample_1_pathway_abundances.tabular"/> + </repeat> + <repeat name="samples"> + <param name="sample_name" value="sample2"/> + <param name="charact_input_fp" value="sample_2_pathway_abundances.tabular"/> + </repeat> + <param name="most_abundant_characteristics_to_extract" value="10"/> + <output name="more_abundant_output_file"> + <assert_contents> + <has_n_columns n="4"/> + <has_n_lines n="16"/> + <has_text text="aerobic respiration I |g__Rhodobacter.s__Rhodobacter_sphaeroides"/> + <has_text text="phytol degradation|g__Staphylococcus.s__Staphylococcus_aureus"/> + </assert_contents> + </output> + <output name="similar_output_file"> + <assert_contents> + <has_n_columns n="4"/> + <has_n_lines n="1921"/> + <has_text text="superpathway of sulfur amino acid biosynthesis |g__Staphylococcus.s__Staphylococcus_epidermidis"/> + <has_text text="tetrapyrrole biosynthesis I |g__Pseudomonas.s__Pseudomonas_aeruginosa"/> + </assert_contents> + </output> + <output name="log"> + <assert_contents> + <has_n_lines n="12"/> + <has_line line="Similar between all samples: 1920"/> + <has_line line=" Number of specific characteristics: 392"/> + <has_line line=" Number of specific characteristics: 1335"/> + </assert_contents> + </output> <output_collection name="specific_files" type="list"> - <element name="specific_to_sample1" file="sample_1_specific_pathways.txt" /> - <element name="specific_to_sample2" file="sample_2_specific_pathways.txt" /> + <element name="specific_to_sample1"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="393"/> + <has_text text="GLUCOSE1PMETAB-PWY"/> + <has_text text="inosine 5 phosphate biosynthesis III|g__Staphylococcus.s__Staphylococcus_aureus"/> + </assert_contents> + </element> + <element name="specific_to_sample2"> + <assert_contents> + <has_n_columns n="3"/> + <has_n_lines n="1336"/> + <has_text text="PEPTIDOGLYCANSYN-PWY"/> + <has_text text="nitrate reduction V |g__Deinococcus.s__Deinococcus_radiodurans"/> + </assert_contents> + </element> </output_collection> </test> </tests> - <help><![CDATA[ **What it does** @@ -80,7 +100,4 @@ * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics ]]></help> - - <citations> - </citations> </tool> \ No newline at end of file