changeset 10:a749062bc435 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty

--- a/humann2.xml	Thu Mar 31 03:35:17 2016 -0400
+++ b/humann2.xml	Tue Apr 12 03:06:03 2016 -0400
@@ -36,10 +36,12 @@
             #set $db = $nucleotide_database.value
             --nucleotide-database $data_table[$db]
 
-            --metaphlan \${METAPHLAN2_DIR}/
-            --metaphlan-options "-t rel_ab"
-            --bowtie2 \${PATH}
-            --diamond \${PATH}
+            #set $mpa_pkl_table = dict([(_[0], _[2]) for _ in $mpa_pkl.input.options.tool_data_table.data])
+            #set $mpa_pkl_db = $mpa_pkl.value
+
+            #set $bowtie2_table = dict([(_[0], _[2]) for _ in $bowtie2db.input.options.tool_data_table.data])
+            #set $bowtie2_db = $bowtie2db.value
+            --metaphlan-options="-t rel_ab --mpa_pkl $mpa_pkl_table[$mpa_pkl_db] --bowtie2db $bowtie2_table[$bowtie2_db]"
 
             --threads \${GALAXY_SLOTS:-4}
 
@@ -69,6 +71,14 @@
             <when value="false" />
         </conditional>
 
+        <param name="mpa_pkl" label="Metadata for MetaPhlAn2" type="select" >
+            <options from_data_table="metaphlan2_metadata" />
+        </param>
+
+        <param name="bowtie2db" label="BowTie2 database for MetaPhlAn2" type="select" >
+            <options from_data_table="metaphlan2_bowtie_db" />
+        </param>
+
         <param name="nucleotide_database" label="Nucleotide database" type="select" >
             <options from_data_table="humann2_nucleotide_database" />
         </param>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan2_bowtie_db.loc.sample	Tue Apr 12 03:06:03 2016 -0400
@@ -0,0 +1,5 @@
+# Bowtie2 db have to be downloaded from https://bitbucket.org/biobakery/metaphlan2/src/5424bb911dfc/db_v20/?at=default (whole directory)
+#
+#Since MetaPhlAn comes bundled with 1 Bowtie2 database, you can use it
+#by downloading it as explained above and uncommenting the following lines.
+#bowtie_db_v20 Defaut BowTie2 database  $METAPHLAN2_DIR/db_v20/mpa_v20_m200

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan2_metadata.loc.sample	Tue Apr 12 03:06:03 2016 -0400
@@ -0,0 +1,5 @@
+#Metadata have to be downloaded from https://bitbucket.org/biobakery/metaphlan2/raw/5424bb911dfcdb7212ea0949d4faeb6e69cfa61f/db_v20/mpa_v20_m200.pkl
+#
+#Since MetaPhlAn comes bundled with 1 metadata database, you can use it
+#by downloading it as explained above and uncommenting the following lines.
+#metadata_db_v20	Defaut MetaPhlAn2 metadata	$METAPHLAN2_DIR/db_v20/mpa_v20_m200.pkl

--- a/tool_data_table_conf.xml.sample	Thu Mar 31 03:35:17 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Apr 12 03:06:03 2016 -0400
@@ -8,4 +8,12 @@
         <columns>value, name, path</columns>
         <file path="tool-data/humann2_nucleotide_database.loc" />
     </table>
+    <table name="metaphlan2_metadata" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/metaphlan2_metadata.loc" />
+    </table>
+    <table name="metaphlan2_bowtie_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/metaphlan2_bowtie_db.loc" />
+    </table>
 </tables>

--- a/tool_dependencies.xml	Thu Mar 31 03:35:17 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 12 03:06:03 2016 -0400
@@ -4,7 +4,7 @@
         <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="metaphlan2" version="2.2.0">
-        <repository changeset_revision="bbac0ef27bb2" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="3cb6227f905e" name="package_metaphlan2_2_2_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="diamond" version="0.7.10">
         <repository changeset_revision="f3f009bdca19" name="package_diamond_0_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />