# HG changeset patch # User ulfschaefer # Date 1468404778 14400 # Node ID 653407a0018eb932fb1505e9f6852cfe32bb0891 Uploaded diff -r 000000000000 -r 653407a0018e MOST.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MOST.sh Wed Jul 13 06:12:58 2016 -0400 @@ -0,0 +1,29 @@ +#!/bin/bash + +echo $@ + +FWDFILE=$1 +shift +REVFILE=$1 +shift +OUTXML=$1 +shift +OUTCSV=$1 +shift +ORGANISM=$1 + +OUTFOLDER=$(mktemp -d --tmpdir tmpMOST_XXXXXXXXXXXXXXXXXXXX) +rm -rf $OUTFOLDER # MOST insists on creating the folder itself + +CMD="MOST.py -1 $FWDFILE -2 $REVFILE -o $OUTFOLDER -st $ORGANISM" + +echo $CMD +eval $CMD + +STEM=$(basename $FWDFILE) +STEM="${STEM%.*}" + +mv $OUTFOLDER"/"$STEM"_MLST_result.csv" $OUTCSV +mv "$OUTFOLDER/$STEM.results.xml" $OUTXML + +rm -rf $OUTFOLDER diff -r 000000000000 -r 653407a0018e MOST.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MOST.xml Wed Jul 13 06:12:58 2016 -0400 @@ -0,0 +1,49 @@ + + Determine MLST from sequencing reads + + + python + lxml + pyyaml + numpy + biopython + bowtie2 + samtools + emboss + blast+ + phemost + + + + MOST.sh + $fwd_file + $rev_file + $out1 + $out2 + "${organism.fields.file_path}" + + + + + + + + + + + + + + + + + + + + + + + + https://github.com/phe-bioinformatics/MOST + + diff -r 000000000000 -r 653407a0018e tool-data/mlst_data.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mlst_data.loc.sample Wed Jul 13 06:12:58 2016 -0400 @@ -0,0 +1,7 @@ +#This file contains entries that point to available MLST data +#It has 5 columns separated by a tab character +#value species name +#dbkey species name +#name Species name + time stamp to be shown in table, eg. Klebsiella pneumoniae-20160707142859 +#time_stamp when the data was downloaded +#file_path absolute path to there allele fastas, profile.txt and reference are stored diff -r 000000000000 -r 653407a0018e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jul 13 06:12:58 2016 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, time_stamp, file_path + +
+
diff -r 000000000000 -r 653407a0018e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jul 13 06:12:58 2016 -0400 @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +