# HG changeset patch
# User bebatut
# Date 1488464707 18000
# Node ID 2caada2d49bccc527abc558c5444a7e4f23d5778
# Parent  156f73f155e30a7070af474dcc89922993889457
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'adf695285ea7366d6c5d48e416c4e00d83b9e733\n'-dirty

diff -r 156f73f155e3 -r 2caada2d49bc humann2.xml
--- a/humann2.xml	Thu Mar 02 03:36:58 2017 -0500
+++ b/humann2.xml	Thu Mar 02 09:25:07 2017 -0500
@@ -1,10 +1,8 @@
 <tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.0">
     <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
-
     <macros>
         <import>humann2_macros.xml</import>
     </macros>
-
     <expand macro="requirements">        
         <requirement type="package" version="2.3.0">bowtie2</requirement>
         <requirement type="package" version="2.6.0">metaphlan2</requirement>
@@ -13,10 +11,8 @@
         <requirement type="package" version="2.7.10">python</requirement>
     </expand>
     <expand macro="stdio"/>
-
     <version_command><![CDATA[ humann2 --version ]]>
     </version_command>
-
     <command><![CDATA[
         #if $nucleotide_db.nucleotide_db_selector == "history"
             mkdir nucleotide_db
@@ -114,7 +110,6 @@
             $remove_column_description_output
             --pathways '$pathways'            
     ]]></command>
-
     <inputs>
         <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom" label="Input sequence file" help=""/>
         <param name='bypass_prescreen' argument='--bypass-prescreen' type='boolean' checked="false" truevalue='--bypass-prescreen' falsevalue='' label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
@@ -127,7 +122,7 @@
                 <option value="history">From history (as collection)</option>
             </param>
             <when value="cached">
-                <param name="nucleotide_database" type="select" label="Nucleotide database" help="">
+                <param name="nucleotide_database" type="select" label="Nucleotide database">
                     <options from_data_table="humann2_nucleotide_database"/>
                 </param>
             </when>
@@ -142,7 +137,7 @@
                 <option value="history">From history</option>
             </param>
             <when value="cached">
-                <param name="protein_database" type="select" label="Protein database" help="">
+                <param name="protein_database" type="select" label="Protein database">
                     <options from_data_table="humann2_protein_database"/>
                 </param>
             </when>
@@ -206,7 +201,6 @@
             <option value="unipathway">UniPathway</option>
         </param>
     </inputs>
-
     <outputs>
         <data format="tsv" name="gene_families_tsv" from_work_dir="output/humann2_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
             <filter>output_format == "tsv"</filter>
@@ -227,7 +221,6 @@
             <filter>output_format == "biom"</filter>
         </data>
     </outputs>
-
     <tests>
         <test>
             <param name="input" value="input_sequences.fasta"/>
@@ -336,7 +329,6 @@
             </output>
         </test>
     </tests>
-
     <help><![CDATA[
 **What it does**
 
@@ -381,6 +373,5 @@
  - A file with pathways and their coverage
 
     ]]></help>
-
     <expand macro="citations"/>
 </tool>
diff -r 156f73f155e3 -r 2caada2d49bc repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Mar 02 03:36:58 2017 -0500
+++ b/repository_dependencies.xml	Thu Mar 02 09:25:07 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="This requires the HUMAnN2 data manager definition to install all required databases.">
     <repository changeset_revision="8602983cb86f" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="71114ccf1026" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="a0eed08a6b61" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>