From f9ba8532b1a8f5fe9f58a9eafd0f45d114730f35 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 20 Jan 2021 16:23:08 +0100
Subject: [PATCH 1/3] add py requirement and actually output

---
 .../combine_metaphlan2_humann2.xml                | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml b/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml
index 960a426..cbd9a69 100644
--- a/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml
+++ b/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml
@@ -1,6 +1,7 @@
 <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>
+        <requirement type="package" version="2.7.18">python</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -8,15 +9,15 @@
     </stdio>
     <version_command></version_command>
     <command><![CDATA[
-        python $__tool_directory__/combine_metaphlan2_humann2.py 
-            --metaphlan2_fp '$metaphlan2_file'
-            --humann2_fp '$humann2_file'
-            --type '$type'   
+        python '$__tool_directory__/combine_metaphlan2_humann2.py'
+            --metaphlan2_file '$metaphlan2_file'
+            --humann2_file '$humann2_file'
+            --type $type    
 
             #if str($type) == 'gene_families'
-                --output_fp '$gene_families_output_file'
+                --output_file '$gene_families_output_file'
             #else
-                --output_fp '$pathway_output_file'
+                --output_file '$pathway_output_file'
             #end if
     ]]></command>
     <inputs>
@@ -78,4 +79,4 @@ of corresponding species and genus.
     ]]></help>
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>

From cb42d33a64670646a3db504c9ce2183480d5fae4 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 25 Jan 2021 17:24:35 +0100
Subject: [PATCH 2/3] add python 3 requirement

and fix parameter names
---
 .../combine_metaphlan2_humann2.xml                     | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml b/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml
index cbd9a69..5b07963 100644
--- a/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml
+++ b/tools/combine_metaphlan2_humann2/combine_metaphlan2_humann2.xml
@@ -1,7 +1,7 @@
 <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>
-        <requirement type="package" version="2.7.18">python</requirement>
+        <requirement type="package" version="3.7">python</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -10,14 +10,14 @@
     <version_command></version_command>
     <command><![CDATA[
         python '$__tool_directory__/combine_metaphlan2_humann2.py'
-            --metaphlan2_file '$metaphlan2_file'
-            --humann2_file '$humann2_file'
+            --metaphlan2_fp '$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>

From b47ecc48ba9001f323338cb691274ed3d643bbb3 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 25 Jan 2021 17:57:22 +0100
Subject: [PATCH 3/3] enable testing

---
 .tt_blacklist | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.tt_blacklist b/.tt_blacklist
index 8b50fa7..fbe4251 100644
--- a/.tt_blacklist
+++ b/.tt_blacklist
@@ -1,5 +1,4 @@
 tools/cdhit
-tools/combine_metaphlan2_humann2
 tools/compare_humann2_output
 tools/compute_wilcoxon_test
 tools/convert_extract_sequence_file