changeset 15:4e2b75051020 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'38ee3fbdc89e93fa2266e9a4e755a086bf564cc6\n'-dirty

--- a/humann2.xml	Mon Feb 20 11:38:51 2017 -0500
+++ b/humann2.xml	Wed Mar 01 11:33:19 2017 -0500
@@ -5,11 +5,12 @@
         <import>humann2_macros.xml</import>
     </macros>
 
-    <expand macro="requirements">
-        <requirement type="package" version="2.2.5">bowtie2</requirement>
+    <expand macro="requirements">        
+        <requirement type="package" version="2.3.0">bowtie2</requirement>
         <requirement type="package" version="2.5.0">metaphlan2</requirement>
         <requirement type="package" version="0.8.24">diamond</requirement>
         <requirement type="package" version="2.24">rapsearch</requirement>
+        <requirement type="package" version="2.7.10">python</requirement>
     </expand>
     <expand macro="stdio"/>
 
@@ -43,16 +44,16 @@
         #end if
 
         #if $taxo_profile.taxonomic_profile_test == "false"
-          #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
-              mkdir ref_db
-              &&
-              bowtie2-build '$taxo_profile.metaphlan2_db_choice.metaphlan2_db_sequences ref_db/ref_db'
-              &&
-              python '$__tool_directory__/transform_json_to_pkl.py'
-                  --json_input '$metaphlan2_db_metadata'
-                  --pkl_output 'ref_db/metadata.pkl'
-              &&
-          #end if
+            #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
+                mkdir ref_db
+                &&
+                bowtie2-build '$taxo_profile.metaphlan2_db_choice.metaphlan2_db_sequences ref_db/ref_db'
+                &&
+                python '$__tool_directory__/transform_json_to_pkl.py'
+                    --json_input '$metaphlan2_db_metadata'
+                    --pkl_output 'ref_db/metadata.pkl'
+                &&
+            #end if
         #end if
 
         humann2
@@ -73,6 +74,10 @@
                 #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
                     #set $metaphlan_option += " --bowtie2db " + ref_db/ref_db
                     #set $metaphlan_option += " --mpa_pkl " + ref_db/metadata.pkl
+                #else
+                    #set $path = $db.cached_db.fields.path
+                    --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'`
+                    --mpa_pkl `ls $path/*.pkl`
                 #end if
             #end if
             --metaphlan-options="$metaphlan_option"
@@ -183,7 +188,11 @@
                         <option value="history">From history</option>
                     </param>
 
-                    <when value="cached"/>
+                    <when value="cached">
+                        <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
+                            <options from_data_table="metaphlan2_database" />
+                        </param>
+                    </when>
                     <when value="history">
                         <param name="metaphlan2_db_sequences" type="data" format="fasta" label="Database with clade-specific marker genes from history" help="(--bowtie2db)"/>
                         <param name="metaphlan2_db_metadata" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history" help="(--mpa_pkl)"/>

--- a/repository_dependencies.xml	Mon Feb 20 11:38:51 2017 -0500
+++ b/repository_dependencies.xml	Wed Mar 01 11:33:19 2017 -0500
@@ -1,4 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="This requires the HUMAnN2 data manager definition to install all required databases.">
-    <repository changeset_revision="332cb1b3b349" name="data_manager_humann2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <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" />
 </repositories>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan2_database.loc.sample	Wed Mar 01 11:33:19 2017 -0500
@@ -0,0 +1,4 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters)
+#02_16_2014	 MetaPhlAn2 clade-specific marker genes	db_v20	/path/to/data
\ No newline at end of file

--- a/tool_data_table_conf.xml.sample	Mon Feb 20 11:38:51 2017 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Mar 01 11:33:19 2017 -0500
@@ -1,4 +1,8 @@
 <tables>
+    <table name="metaphlan2_database" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/metaphlan2_database.loc" />
+    </table>
     <table name="humann2_nucleotide_database" comment_char="#">
         <columns>value, name, dbkey, path</columns>
         <file path="tool-data/humann2_nucleotide_database.loc" />