# 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 @@ + + + + value, name, path + +
+
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