Mercurial > repos > bebatut > group_humann2_uniref_abundances_to_go
changeset 1:8d3dec059275 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719-dirty
| author | bebatut |
|---|---|
| date | Mon, 22 Feb 2016 09:43:44 -0500 |
| parents | 13df6c6647fb |
| children | 64ef7636d315 |
| files | download_datasets.sh group_humann2_uniref_abundances_to_go.xml tool_dependencies.xml |
| diffstat | 3 files changed, 10 insertions(+), 34 deletions(-) [+] |
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--- a/download_datasets.sh Mon Feb 22 07:11:20 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#!/bin/bash - -MY_PATH=`dirname "$0"` -data_dir=$MY_PATH"/data/" - -if [ ! -d $data_dir ]; then - mkdir $data_dir -fi - -cd $data_dir - -echo "Download required databases" -echo "===========================" - -if [ ! -f "go.obo" ]; then - echo "Download basic Gene Ontology..." - wget http://geneontology.org/ontology/go.obo -fi -if [ ! -f "goslim_metagenomics.obo" ]; then - echo "Download metagenomic slim Gene Ontology..." - wget http://www.geneontology.org/ontology/subsets/goslim_metagenomics.obo -fi - -if [ ! -f "map_infogo1000_uniref50.txt" ]; then - echo "Download humann2 correspondance between Uniref50 and GO" - wget https://bitbucket.org/biobakery/humann2/raw/d1ac153083d48a5384e3b3d3597b9e36b1a4606e/humann2/data/misc/map_infogo1000_uniref50.txt.gz - gunzip map_infogo1000_uniref50.txt.gz -fi - -echo "" \ No newline at end of file
--- a/group_humann2_uniref_abundances_to_go.xml Mon Feb 22 07:11:20 2016 -0500 +++ b/group_humann2_uniref_abundances_to_go.xml Mon Feb 22 09:43:44 2016 -0500 @@ -25,7 +25,9 @@ <command><![CDATA[ \${GROUP_UNIREF_GO_DIR}/group_to_GO_abundances.sh -i $humann2_gene_families_abundance - -o $go_slim_term_abundance + -m $molecular_function_abundance + -b $biological_process_abundance + -c $cellular_component_abundance #if $gene_ontology.gene_ontology_test: -a $gene_ontology.gene_ontology_file @@ -89,8 +91,12 @@ </inputs> <outputs> - <data format="tsv" name="go_slim_term_abundance" - label="${tool.name} on ${on_string}: GO slim abundance"/> + <data format="tabular" name="molecular_function_abundance" + label="${tool.name} on ${on_string}: Molecular function abundance"/> + <data format="tabular" name="biological_process_abundance" + label="${tool.name} on ${on_string}: Biological process abundance"/> + <data format="tabular" name="cellular_component_abundance" + label="${tool.name} on ${on_string}: Cellular component abundance"/> </outputs> <tests>
--- a/tool_dependencies.xml Mon Feb 22 07:11:20 2016 -0500 +++ b/tool_dependencies.xml Mon Feb 22 09:43:44 2016 -0500 @@ -12,7 +12,7 @@ <package name="group_humann2_uniref_abundances_to_GO" version="0.1"> <install version="1.0"> <actions> - <action type="download_by_url">https://github.com/ASaiM/group_humann2_uniref_abundances_to_GO/archive/v0.1.5.zip</action> + <action type="download_by_url">https://github.com/ASaiM/group_humann2_uniref_abundances_to_GO/archive/v0.2.1.zip</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR/</destination_directory>