# HG changeset patch
# User bebatut
# Date 1460444763 14400
# Node ID a749062bc4354c5a0aab6f53b292980380b2631f
# Parent 7d2be77d5b83defd2bdc99a7fe45dfefa12879bc
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
diff -r 7d2be77d5b83 -r a749062bc435 humann2.xml
--- 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 @@
+
+
+
+
+
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+
+
diff -r 7d2be77d5b83 -r a749062bc435 tool-data/metaphlan2_bowtie_db.loc.sample
--- /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
diff -r 7d2be77d5b83 -r a749062bc435 tool-data/metaphlan2_metadata.loc.sample
--- /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
diff -r 7d2be77d5b83 -r a749062bc435 tool_data_table_conf.xml.sample
--- 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 @@
value, name, path
+
+
diff -r 7d2be77d5b83 -r a749062bc435 tool_dependencies.xml
--- 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 @@
-
+