Mercurial > repos > bebatut > combine_metaphlan2_humann2
diff combine_metaphlan2_humann2.xml @ 1:e25efca0a49c draft
"planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9"
author | bebatut |
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date | Mon, 14 Sep 2020 12:19:49 +0000 |
parents | 31394a0c0242 |
children |
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--- a/combine_metaphlan2_humann2.xml Fri Apr 15 09:15:21 2016 -0400 +++ b/combine_metaphlan2_humann2.xml Mon Sep 14 12:19:49 2020 +0000 @@ -1,40 +1,32 @@ -<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0"> +<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.2.0"> <description>to relate genus/species abundances and gene families/pathways abundances</description> - <requirements> </requirements> - <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> - <version_command></version_command> - <command><![CDATA[ python $__tool_directory__/combine_metaphlan2_humann2.py - --metaphlan2_file $metaphlan2_file - --humann2_file $humann2_file - --type $type + --metaphlan2_fp '$metaphlan2_file' + --humann2_fp '$humann2_file' + --type '$type' #if str($type) == 'gene_families' - --output_file $gene_families_output_file + --output_fp '$gene_families_output_file' #else - --output_file $pathway_output_file + --output_fp '$pathway_output_file' #end if ]]></command> - <inputs> <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/> - <param name="humann2_file" 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 with corresponding taxonomic stratification (--humann2_file)"/> - <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)"> <option value="gene_families" selected="true">Gene families</option> <option value="pathways">Pathways</option> </param> </inputs> - <outputs> <data name="gene_families_output_file" format="tabular" label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" > @@ -45,30 +37,45 @@ <filter>type=="pathways"</filter> </data> </outputs> - <tests> <test> - <param name="metaphlan2_file" value="metaphlan2_input.txt"/> - <param name="humann2_file" value="humann2_gene_families_input.tabular"/> - <param name='type' value="gene_families"/> - <output name="gene_families_output_file" file="gene_families_output.tabular"/> + <param name="metaphlan2_file" value="metaphlan2_input.txt"/> + <param name="humann2_file" value="humann2_gene_families_input.tabular"/> + <param name='type' value="gene_families"/> + <output name="gene_families_output_file"> + <assert_contents> + <has_n_columns n="8"/> + <has_n_lines n="29434"/> + <has_text text="Staphylococcus_epidermidis"/> + <has_text text="Putative transposon Tn552 DNA invertase bin3"/> + <has_size value="3467947"/> + </assert_contents> + </output> </test> <test> <param name="metaphlan2_file" value="metaphlan2_input.txt"/> <param name="humann2_file" value="humann2_pathways_input.tabular"/> <param name='type' value="pathways"/> - <output name="pathway_output_file" file="pathways_output.tabular"/> + <output name="pathway_output_file"> + <assert_contents> + <has_n_columns n="8"/> + <has_n_lines n="1533"/> + <has_text text="Rhodobacter_sphaeroides"/> + <has_text text="superpathway of acetyl CoA biosynthesis"/> + <has_size value="186363"/> + </assert_contents> + </output> </test> </tests> - <help><![CDATA[ **What it does** This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs. -For each gene families/pathways and the corresponding taxonomic stratification, you get relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus. +For each gene families/pathways and the corresponding taxonomic stratification, +you get relative abundance of this gene family/pathway and the relative abundance +of corresponding species and genus. ]]></help> - <citations> </citations> </tool> \ No newline at end of file