# HG changeset patch
# User thanhlv
# Date 1645611466 0
# Node ID d1df295495a9ddf184ef08288f8be02e41297e85
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metamlst commit 041ede79a8b699b00b1106cc82a5efe3c90c9876-dirty"
diff -r 000000000000 -r d1df295495a9 metamlst.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metamlst.xml Wed Feb 23 10:17:46 2022 +0000
@@ -0,0 +1,379 @@
+
+ performs an in-silico Multi Locus Sequence Typing (MLST) Analysis on metagenomic samples
+
+ 1.2.2
+
+
+ metamlst
+
+ metamlst.py --version | head -n 1 | cut -f 2
+ ${read1}.bam &&
+ metamlst.py
+ #if $filter_species.filter=='yes'
+ #set species_list = ",".join([$species for $species in $filter_species.species])
+ --filter $species_list
+ #end if
+ --penalty $penalty
+ --minscore $minscore
+ --max_xM $max_xm
+ --min_read_len $min_read_len
+ --min_accuracy $min_accuracy
+ --nloci $nloci
+ $log
+ $write_sequences
+ ${read1}.bam
+ -o ./out
+ -d '$metamlstdb.fields.path' &&
+ metamlst-merge.py ./out -d '$metamlstdb.fields.path' &&
+ #if $log
+ cat ./out/*.out > log.txt &&
+ #end if
+ #if $write_sequences
+ cat ./out/*.nfo > sequences.txt
+ #end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ log == True
+
+
+ write_sequences == True
+
+
+
+
+
+ 10.1093/nar/gkw837
+
+
diff -r 000000000000 -r d1df295495a9 tool-data/metamlstdb.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metamlstdb.loc Wed Feb 23 10:17:46 2022 +0000
@@ -0,0 +1,1 @@
+metamlstDB_2021 metamlstDB_2021 /home/ubuntu/galaxy-tools/tools/metamlst/metamlstDB_2021.db
\ No newline at end of file
diff -r 000000000000 -r d1df295495a9 tool-data/metamlstdb.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metamlstdb.loc.sample Wed Feb 23 10:17:46 2022 +0000
@@ -0,0 +1,2 @@
+# bowtie2_indices.loc.sample
+#
\ No newline at end of file
diff -r 000000000000 -r d1df295495a9 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Feb 23 10:17:46 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+
\ No newline at end of file