# HG changeset patch
# User ulfschaefer
# Date 1467988495 14400
# Node ID a984d5b727d8b778e878d780ee7a26607a1f0c76
# Parent 2e0e0e1963862d2691d9a15ce02c66b3a9ad8dba
Uploaded
diff -r 2e0e0e196386 -r a984d5b727d8 MOST.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MOST.sh Fri Jul 08 10:34:55 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 2e0e0e196386 -r a984d5b727d8 MOST.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MOST.xml Fri Jul 08 10:34:55 2016 -0400
@@ -0,0 +1,49 @@
+
+ Determine MLST from sequencing reads
+
+
+ python
+ lxml
+ pyyaml
+ numpy
+ biopython
+ bowtie2
+ samtools
+ emboss
+ blast_plus
+ phemost
+
+
+
+ MOST.sh
+ $fwd_file
+ $rev_file
+ $out1
+ $out2
+ "${organism.fields.file_path}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ https://github.com/phe-bioinformatics/MOST
+
+
diff -r 2e0e0e196386 -r a984d5b727d8 tool-data/mlst_data.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mlst_data.loc.sample Fri Jul 08 10:34:55 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 2e0e0e196386 -r a984d5b727d8 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Jul 08 10:34:55 2016 -0400
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, time_stamp, file_path
+
+
+
diff -r 2e0e0e196386 -r a984d5b727d8 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jul 08 10:34:55 2016 -0400
@@ -0,0 +1,33 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+