# HG changeset patch
# User bebatut
# Date 1456142985 18000
# Node ID 0d3d44f13122eaefb1a204d87af2a99450ea42a3
# Parent  d084f63fbf30a827be591ca75b98c78356206335
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 313952cc4a20e8fb82380bfbf5ede26217197719

diff -r d084f63fbf30 -r 0d3d44f13122 humann2.xml
--- a/humann2.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/humann2.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,16 +14,12 @@
 
     <version_command>
 <![CDATA[
-    humann2 --version
+    \${HUMANN2_DIR}/humann2 --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        (which diamond || exit 200)
-
-        && 
-
-        humann2 
+        \${HUMANN2_DIR}/humann2 
             -i "$input_file"
         
             #if $taxonomic_profile.taxonomic_profile_test:
diff -r d084f63fbf30 -r 0d3d44f13122 humann2_join_tables.xml
--- a/humann2_join_tables.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/humann2_join_tables.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,7 +14,7 @@
 
     <version_command>
 <![CDATA[
-    humann2_join_tables --version
+    \${HUMANN2_DIR}/humann2_join_tables --version
 ]]>
     </version_command>
 
@@ -27,7 +27,7 @@
         #end for
 
         && 
-        humann2_join_tables
+        \${HUMANN2_DIR}/humann2_join_tables
             -i "tmp_dir"
             -o $joined_table           
     ]]></command>
diff -r d084f63fbf30 -r 0d3d44f13122 humann2_reduce_table.xml
--- a/humann2_reduce_table.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/humann2_reduce_table.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,12 +14,12 @@
 
     <version_command>
 <![CDATA[
-    humann2_reduce_table --version
+    \${HUMANN2_DIR}/humann2_reduce_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        humann2_reduce_table
+        \${HUMANN2_DIR}/humann2_reduce_table
             -i $input_table
             -o $output_table
             --function $function
diff -r d084f63fbf30 -r 0d3d44f13122 humann2_regroup_table.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_regroup_table.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -0,0 +1,91 @@
+<tool id="humann2_regroup_table" name="Regroup HUMAnN2 table features" version="0.1.0">
+    <description></description>
+
+    <requirements>
+        <requirement type="package" version="2.2.4">bowtie2</requirement>
+        <requirement type="package" version="2.0">metaphlan2</requirement>
+        <requirement type="package" version="0.6.13">diamond</requirement>
+        <requirement type="package" version="2.0">humann2</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <version_command>
+<![CDATA[
+    \${HUMANN2_DIR}/humann2_regroup_table --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        \${HUMANN2_DIR}/humann2_regroup_table
+            -i $input_table
+            -o $output_table
+            --function $function
+
+            #if $built_in.test:
+                --groups $built_in.groups
+            #else:
+                --custom $built_in.file
+                $built_in.reversed
+            #end if  
+    ]]></command>
+
+    <inputs>
+        <param name="input_table" type="data" format="tsv" label="Gene/pathway 
+            table" help=""/>
+
+        <param name="function" type="select" label="How to combine grouped features?" help="(--function)">
+            <option value="sum" selected="true">Sum</option>
+            <option value="mean">Mean</option>
+        </param>
+
+        <conditional name="built_in">
+            <param name='test' type='boolean' checked="false" truevalue='true' 
+                falsevalue='false' label="Use built-in grouping options?" 
+                help=""/>
+            <when value="true">
+                <param name="groups" type="select" label="Grouping options" help="(--groups)">
+                    <option value="uniref50_ec" selected="true">Collapses UniRef50 gene families into top level enzyme commission (EC) categories (associations inferred from UniProt)</option>
+                    <option value="uniref50_go">Collapses UniRef50 gene families into a subset of non-redundant, high-level Gene Ontology (GO) categories (associations inferred from UniProt and a HUMAnN2-specific parsing of the GO hierarchy)</option>
+                    <option value="uniref50_ko">Collapses UniRef50 gene fammilies into KEGG Orthogroups (KOs) (associations inferred from UniProt)</option>
+                    <option value="uniref50_rxn">Collapses UniRef50 gene families into metacyc reactions (use of reaction abundances to compute the abundance and coverage of broader metabolic pathways)</option>
+                </param>
+            </when>
+            <when value="false">
+                <param name="file" type="data" format="tsv" label="Custom groups file" help="(--custom)"/>
+                <param name='reversed' type='boolean' checked="false" truevalue='--reversed' 
+                    falsevalue='' label="Is the groups file reversed?" 
+                    help="Mapping from features to groups. (--reversed)"/>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="output_table" label="Regrouped table for 
+            ${on_string} (HUMAnN2)" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
+            <param name="function" value="sum"/>
+            <param name="test" value="true"/>
+            <param name="groups" value="uniref50_ec"/>
+            <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        Regroup HUMAnN2 table features is a tool for egrouping table features. Given a table of feature values and a mapping of groups to component features, produce a new table with group values in place of feature values.
+
+        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
diff -r d084f63fbf30 -r 0d3d44f13122 humann2_rename_table.xml
--- a/humann2_rename_table.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/humann2_rename_table.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,12 +14,12 @@
 
     <version_command>
 <![CDATA[
-    humann2_rename_table --version
+    \${HUMANN2_DIR}/humann2_rename_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        humann2_rename_table
+        \${HUMANN2_DIR}/humann2_rename_table
             -i $input_table
             -o $output_table
 
diff -r d084f63fbf30 -r 0d3d44f13122 humann2_renorm_table.xml
--- a/humann2_renorm_table.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/humann2_renorm_table.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,12 +14,12 @@
 
     <version_command>
 <![CDATA[
-    humann2_renorm_table --version
+    \${HUMANN2_DIR}/humann2_renorm_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        humann2_renorm_table
+        \${HUMANN2_DIR}/humann2_renorm_table
             -i $input_table
             -o $output_table
             --norm $norm
diff -r d084f63fbf30 -r 0d3d44f13122 in_development/humann2_merge_abundance_tables.xml
--- a/in_development/humann2_merge_abundance_tables.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/in_development/humann2_merge_abundance_tables.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,12 +14,12 @@
 
     <version_command>
 <![CDATA[
-    humann2_merge_abundance_tables --version
+    \${HUMANN2_DIR}/humann2_merge_abundance_tables --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        humann2_merge_abundance_tables
+        \${HUMANN2_DIR}/humann2_merge_abundance_tables
             --input-genes $input_gene
             --input-pathways $input_pathway
             --gene-mapping $gene_mapping
diff -r d084f63fbf30 -r 0d3d44f13122 in_development/humann2_regroup_table.xml
--- a/in_development/humann2_regroup_table.xml	Fri Dec 18 09:04:07 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-<tool id="humann2_regroup_table" name="Regroup HUMAnN2 table features" version="0.1.0">
-    <description></description>
-
-    <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-        <requirement type="package" version="2.0">humann2</requirement>
-    </requirements>
-
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-
-    <version_command>
-<![CDATA[
-    humann2_regroup_table --version
-]]>
-    </version_command>
-
-    <command><![CDATA[
-        humann2_regroup_table
-            -i $input_table
-            -o $output_table
-            --function $function
-
-            #if $built_in.test:
-                --groups $built_in.groups
-            #else:
-                --custom $built_in.file
-                $built_in.reversed
-            #end if  
-    ]]></command>
-
-    <inputs>
-        <param name="input_table" type="data" format="tsv" label="Gene/pathway 
-            table" help=""/>
-
-        <param name="function" type="select" label="How to combine grouped features?" help="(--function)">
-            <option value="sum" selected="true">Sum</option>
-            <option value="mean">Mean</option>
-        </param>
-
-        <conditional name="built_in">
-            <param name='test' type='boolean' checked="false" truevalue='true' 
-                falsevalue='false' label="Use built-in grouping options?" 
-                help=""/>
-            <when value="true">
-                <param name="groups" type="select" label="Grouping options" help="(--groups)">
-                    <option value="uniref50_ec" selected="true">Collapses UniRef50 gene families into top level enzyme commission (EC) categories (associations inferred from UniProt)</option>
-                    <option value="uniref50_go">Collapses UniRef50 gene families into a subset of non-redundant, high-level Gene Ontology (GO) categories (associations inferred from UniProt and a HUMAnN2-specific parsing of the GO hierarchy)</option>
-                    <option value="uniref50_ko">Collapses UniRef50 gene fammilies into KEGG Orthogroups (KOs) (associations inferred from UniProt)</option>
-                    <option value="uniref50_rxn">Collapses UniRef50 gene families into metacyc reactions (use of reaction abundances to compute the abundance and coverage of broader metabolic pathways)</option>
-                </param>
-            </when>
-            <when value="false">
-                <param name="file" type="data" format="tsv" label="Custom groups file" help="(--custom)"/>
-                <param name='reversed' type='boolean' checked="false" truevalue='--reversed' 
-                    falsevalue='' label="Is the groups file reversed?" 
-                    help="Mapping from features to groups. (--reversed)"/>
-            </when>
-        </conditional>
-    </inputs>
-
-    <outputs>
-        <data format="tsv" name="output_table" label="Regrouped table for 
-            ${on_string} (HUMAnN2)" />
-    </outputs>
-
-    <tests>
-        <test>
-            <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
-            <param name="function" value="sum"/>
-            <param name="test" value="true"/>
-            <param name="groups" value="uniref50_ec"/>
-            <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-        **What it does**
-
-        Regroup HUMAnN2 table features is a tool for egrouping table features. Given a table of feature values and a mapping of groups to component features, produce a new table with group values in place of feature values.
-
-        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
-
-    ]]></help>
-
-    <citations>
-    </citations>
-</tool>
\ No newline at end of file
diff -r d084f63fbf30 -r 0d3d44f13122 in_development/humann2_rna_dna_norm.xml
--- a/in_development/humann2_rna_dna_norm.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/in_development/humann2_rna_dna_norm.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,12 +14,12 @@
 
     <version_command>
 <![CDATA[
-    humann2_rna_dna_norm --version
+    \${HUMANN2_DIR}/humann2_rna_dna_norm --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        humann2_rna_dna_norm
+        \${HUMANN2_DIR}/humann2_rna_dna_norm
             --input_dna $input_dna
             --input_rna $input_rna
             --output_basename "combined"
diff -r d084f63fbf30 -r 0d3d44f13122 in_development/humann2_split_table.xml
--- a/in_development/humann2_split_table.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/in_development/humann2_split_table.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -14,12 +14,12 @@
 
     <version_command>
 <![CDATA[
-    humann2_split_table --version
+    \${HUMANN2_DIR}/humann2_split_table --version
 ]]>
     </version_command>
 
     <command><![CDATA[
-        humann2_split_table
+        \${HUMANN2_DIR}/humann2_split_table
             -i "input_file"
             -o "output"            
     ]]></command>
diff -r d084f63fbf30 -r 0d3d44f13122 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 18 09:04:07 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 07:09:45 2016 -0500
@@ -10,17 +10,6 @@
         <repository changeset_revision="f3f009bdca19" name="package_diamond_0_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="humann2" version="2.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://bitbucket.org/biobakery/humann2/downloads/humann2_v0.5.0.tar.gz</action>
-                <action type="shell_command">python setup.py install --bypass-dependencies-install</action>
-                <action type="make_directory">$INSTALL_DIR/databases</action>
-                <action type="set_environment">
-                    <environment_variable action="set_to" name="HUMANN2_DIR">$INSTALL_DIR/</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme />
+        <repository changeset_revision="abe443d7f9e7" name="package_humann_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>