# HG changeset patch
# User bebatut
# Date 1488293666 18000
# Node ID 99066fa0645ba2c2f3920be5ba6270636002ada1
# Parent  4d1bf99ad5ef21ddfa1048ecd5ad9abaee6bd0cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty

diff -r 4d1bf99ad5ef -r 99066fa0645b metaphlan2.xml
--- a/metaphlan2.xml	Mon Feb 27 06:12:35 2017 -0500
+++ b/metaphlan2.xml	Tue Feb 28 09:54:26 2017 -0500
@@ -20,10 +20,6 @@
 
     <command>
 <![CDATA[
-        (which bowtie2 || exit 200)
-
-        &&
-
         #if $db.db_selector == "history"
             mkdir ref_db
             &&
@@ -143,8 +139,6 @@
         <param argument="--ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?"/>
         <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
         <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
-        <param argument="--sample_id_key" type="text" value="#SampleID" label="Sample ID key"/>
-        <param argument="--sample_id" type="text" value="Metaphlan2_Analysis" label="Sample ID"/>
     </inputs>
 
     <outputs>
@@ -168,8 +162,6 @@
             <param name="ignore_bacteria" value="" />
             <param name="ignore_archaea" value="" />
             <param name="stat_q" value="0.1" />
-            <param name="sample_id_key" value="#SampleID"/>
-            <param name="sample_id" value="Metaphlan2_Analysis"/>
             <output name="output_file" file="community_profile.tabular"/>
         </test>
     </tests>
diff -r 4d1bf99ad5ef -r 99066fa0645b repository_dependencies.xml
--- a/repository_dependencies.xml	Mon Feb 27 06:12:35 2017 -0500
+++ b/repository_dependencies.xml	Tue Feb 28 09:54:26 2017 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases.">
-    <repository changeset_revision="dbfade666d42" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="1d8f4e8ef24c" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>