# HG changeset patch
# User bebatut
# Date 1488443818 18000
# Node ID 156f73f155e30a7070af474dcc89922993889457
# Parent  4b50b1b13b6417ed36a7374ca8cf51a13775696f
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'318eb33ea866441cc9b2f98bdda88dd594037a0e\n'-dirty

diff -r 4b50b1b13b64 -r 156f73f155e3 humann2.xml
--- a/humann2.xml	Wed Mar 01 11:38:23 2017 -0500
+++ b/humann2.xml	Thu Mar 02 03:36:58 2017 -0500
@@ -18,19 +18,17 @@
     </version_command>
 
     <command><![CDATA[
-        mkdir nucleotide_db
-        &&
-
         #if $nucleotide_db.nucleotide_db_selector == "history"
+            mkdir nucleotide_db
+            &&
             #for $file in $nucleotide_db.nucleotide_database:
                 cp '$file' 'nucleotide_db/$file.name' &&
             #end for
         #end if
 
-        mkdir protein_db
-        &&
-
         #if $protein_db.protein_db_selector == "history"
+            mkdir protein_db
+            &&
             #if $translated_alignment == "diamond"
                 diamond makedb
                     --in '$protein_db.protein_database'
@@ -59,12 +57,10 @@
         humann2
             --input '$input'
             -o 'output'
-
             $bypass_prescreen
             $bypass_nucleotide_index
             $bypass_translated_search
             $bypass_nucleotide_search
-
             --annotation-gene-index $annotation_gene_index
 
             #set $metaphlan_option = "-t rel_ab"
@@ -83,13 +79,13 @@
             --metaphlan-options="$metaphlan_option"
 
             #if $nucleotide_db.nucleotide_db_selector == "cached"
-                --nucleotide-database '$nucleotide_db.nucleotide_database'
+                --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'
             #else
                 --nucleotide-database nucleotide_db
             #end if
 
             #if $protein_db.protein_db_selector == "cached"
-                --protein-database '$protein_db.protein_database'
+                --protein-database '$protein_db.protein_database.fields.path'
             #else
                 --protein-database protein_db
             #end if
@@ -111,30 +107,25 @@
             --minpath '$minpath'
             --pick-frames '$pick_frames'
             --gap-fill '$gap_fill'
-
             --output-format '$output_format'
             --output-max-decimals '$output_max_dec'
             --output-basename 'humann2'
             $remove_statified_output
             $remove_column_description_output
-
             --pathways '$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?"/>
         <param name='bypass_nucleotide_index' argument='--bypass-nucleotide-index' type='boolean' checked="false" truevalue='--bypass-nucleotide-index' falsevalue='' label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
         <param name='bypass_translated_search' argument='--bypass-translated-search' type='boolean' checked="false" truevalue='--bypass-translated-search' falsevalue='' label="Bypass the translated search step?"/>
         <param name='bypass_nucleotide_search' argument='--bypass-nucleotide-search' type='boolean' checked="false" truevalue='--bypass-translated-search' falsevalue='' label="Bypass the nucleotide search steps?"/>
-
         <conditional name="nucleotide_db">
             <param name="nucleotide_db_selector" type="select" label="Nucleotide database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
                 <option value="cached" selected="true">Locally cached</option>
                 <option value="history">From history (as collection)</option>
             </param>
-
             <when value="cached">
                 <param name="nucleotide_database" type="select" label="Nucleotide database" help="">
                     <options from_data_table="humann2_nucleotide_database"/>
@@ -144,15 +135,12 @@
                 <param format="fasta" name="nucleotide_database" argument="--nucleotide-database" type="data_collection" collection_type="list" label="Nucleotide database from history" help="Each file must be named: ^[g__].[s__]"/>
             </when>
         </conditional>
-
         <param name="annotation_gene_index" argument="--annotation-gene-index" type="integer" value="8" label="Index of the gene in the sequence annotation"/>
-
         <conditional name="protein_db">
             <param name="protein_db_selector" type="select" label="Protein database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
                 <option value="cached" selected="true">Locally cached</option>
                 <option value="history">From history</option>
             </param>
-
             <when value="cached">
                 <param name="protein_database" type="select" label="Protein database" help="">
                     <options from_data_table="humann2_protein_database"/>
@@ -162,7 +150,6 @@
                 <param name="protein_database" argument="--protein-database" type="data" format="fasta" label="Protein database from history"/>
             </when>
         </conditional>
-
         <param argument="--evalue" type="float" value="1" label="E-value threshold to use with the translated search"/>
         <param name="search_mode" argument="--search-mode" type="select" label="Search for uniref50 or uniref90 gene families?">
             <option value="uniref50" selected="true">uniref50</option>
@@ -172,7 +159,6 @@
         <param name="identity_threshold" argument="--identity-threshold" type="float" value="50" label="Identity threshold for alignments"/>
         <param name="translated_subject_coverage_threshold" argument="--translated-subject-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
         <param name="translated_query_coverage_threshold" argument="--translated-query-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
-
         <conditional name="taxo_profile">
             <param name='taxonomic_profile_test' type='select' label="Use a custom taxonomic profile?" help="The file must have been created by MetaPhlan2">
                 <option value="true">Yes</option>
@@ -187,7 +173,6 @@
                         <option value="cached" selected="true">Default MetaPhlAn2 database</option>
                         <option value="history">From history</option>
                     </param>
-
                     <when value="cached">
                         <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
                             <options from_data_table="metaphlan2_database" />
@@ -200,7 +185,6 @@
                 </conditional>
             </when>
         </conditional>
-
         <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" label="id mapping file for alignments" optional="True"/>
         <param name='translated_alignment' argument="--translated-alignment" type="select" label="Software to use for translated alignment" help="(--pathways)">
             <option value="rapsearch" selected="true">Rapsearch</option>
@@ -217,7 +201,6 @@
         <param name="output_max_dec" type="integer" value="10" label="Number of decimals to output" argument="--output-max-decimals"/>
         <param name='remove_statified_output' type='boolean' checked="false" truevalue='--remove-stratified-output' falsevalue='' label="Remove stratification from output?" argument="--remove-stratified-output"/>
         <param name='remove_column_description_output' type='boolean' checked="false" truevalue='--remove-column-description-output' falsevalue='' label="Remove stratification from output?" argument="--remove-column-description-output"/>
-
         <param name='pathways' type="select" label="Database to use for pathway computations" help="(--pathways)">
             <option value="metacyc" selected="true">MetaCyc</option>
             <option value="unipathway">UniPathway</option>
@@ -231,14 +214,12 @@
         <data format="biom" name="gene_families_biom" from_work_dir="output/humann2_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >
             <filter>output_format == "biom"</filter>
         </data>
-
         <data format="tsv" name="pathcoverage_tsv" from_work_dir="output/humann2_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
             <filter>output_format == "tsv"</filter>
         </data>
         <data format="biom" name="pathcoverage_biom" from_work_dir="output/humann2_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" >
             <filter>output_format == "biom"</filter>
         </data>
-
         <data format="tsv" name="pathabundance_tsv" from_work_dir="output/humann2_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" >
             <filter>output_format == "tsv"</filter>
         </data>
diff -r 4b50b1b13b64 -r 156f73f155e3 repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Mar 01 11:38:23 2017 -0500
+++ b/repository_dependencies.xml	Thu Mar 02 03:36:58 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="7b8c3728d7ca" name="data_manager_humann2_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" />
 </repositories>
diff -r 4b50b1b13b64 -r 156f73f155e3 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Mar 01 11:38:23 2017 -0500
+++ b/tool_data_table_conf.xml.sample	Thu Mar 02 03:36:58 2017 -0500
@@ -1,6 +1,6 @@
 <tables>
     <table name="metaphlan2_database" comment_char="#">
-        <columns>value, name, path</columns>
+        <columns>value, name, dbkey, path</columns>
         <file path="tool-data/metaphlan2_database.loc" />
     </table>
     <table name="humann2_nucleotide_database" comment_char="#">