# HG changeset patch
# User bebatut
# Date 1456152224 18000
# Node ID 8d3dec059275854560b9a8a9cd49772971e4e092
# Parent  13df6c6647fb7715f7deb31e58ff7548e521283d
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/group_humann2_uniref_abundances_to_GO commit 313952cc4a20e8fb82380bfbf5ede26217197719-dirty

diff -r 13df6c6647fb -r 8d3dec059275 download_datasets.sh
--- 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
diff -r 13df6c6647fb -r 8d3dec059275 group_humann2_uniref_abundances_to_go.xml
--- 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>
diff -r 13df6c6647fb -r 8d3dec059275 tool_dependencies.xml
--- 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>