# 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
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+ python
+ lxml
+ pyyaml
+ numpy
+ biopython
+ bowtie2
+ samtools
+ emboss
+ blast+
+ phemost
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+ MOST.sh
+ $fwd_file
+ $rev_file
+ $out1
+ $out2
+ "${organism.fields.file_path}"
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+ https://github.com/phe-bioinformatics/MOST
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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 @@
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+ value, dbkey, name, time_stamp, file_path
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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 @@
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