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changeset 0:653407a0018e draft default tip

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author ulfschaefer
date Wed, 13 Jul 2016 06:12:58 -0400
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files MOST.sh MOST.xml tool-data/mlst_data.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 5 files changed, 125 insertions(+), 0 deletions(-) [+]
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--- /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
--- /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 @@
+<tool id="most" name="MOST">
+	<description>Determine MLST from sequencing reads</description>
+
+    <requirements>
+        <requirement type="package" version="2.7.10">python</requirement>
+        <requirement type="package" version="3.2.3">lxml</requirement>
+        <requirement type="package" version="3.11">pyyaml</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="1.66">biopython</requirement>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="5.0.0">emboss</requirement>
+        <requirement type="package" version="2.2.27">blast+</requirement>
+        <requirement type="package" version="1.0">phemost</requirement>
+    </requirements>
+
+	<command interpreter="bash">
+	MOST.sh
+	$fwd_file
+	$rev_file
+	$out1
+	$out2
+	"${organism.fields.file_path}"
+	</command>
+
+	<inputs>
+        <param name="fwd_file" type="data" format="fastq" label="Read dataset for direction 1" help="Select fastq R1 here."/>
+        <param name="rev_file" type="data" format="fastq" label="Read dataset for direction 2" help="Select fastq R2 here."/>
+        <param name="organism" type="select" label="Select an organism">
+            <options from_data_table="mlst_data">
+                <column name="value" index="0"/>
+                <column name="dbkey" index="1"/>
+                <column name="name" index="2"/>
+                <column name="time_stamp" index="3"/>
+                <column name="file_path" index="4"/>
+                <validator type="no_options" message="No indexes are available" />
+            </options>
+        </param>
+	</inputs>
+
+	<outputs>
+	    <data name="out1" format="xml" label="${fwd_file.name}: MLST result XML"/>
+	    <data name="out2" format="csv" label="${fwd_file.name}: MLST result CSV"/>
+	</outputs>
+
+	<help>
+		https://github.com/phe-bioinformatics/MOST
+	</help>
+</tool>
--- /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
--- /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 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="mlst_data" comment_char="#">
+        <columns>value, dbkey, name, time_stamp, file_path</columns>
+        <file path="tool-data/mlst_data.loc" />
+    </table>
+</tables>
--- /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 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="python" version="2.7.10">
+        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="lxml" version="3.2.3">
+        <repository changeset_revision="bafab0f9cda1" name="package_python_2_7_lxml_3_2_3" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+    <package name="pyyaml" version="3.11">
+        <repository changeset_revision="99267d131c05" name="package_python_2_7_pyyaml_3_11" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+	<package name="biopython" version="1.66">
+        <repository changeset_revision="c722591ee0aa" name="package_python_2_7_biopython_1_66" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+	<package name="bowtie2" version="2.1.0">
+        <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+    <package name="samtools" version="0.1.18">
+        <repository changeset_revision="1409782220c9" name="package_samtools_0_1_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+    <package name="emboss" version="5.0.0">
+        <repository changeset_revision="cf998ddc0542" name="package_emboss_5_0_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+    <package name="blast+" version="2.2.27">
+        <repository changeset_revision="b614c5772f73" name="package_blast_plus_2_2_27" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+	<package name="phemost" version="1.0">
+        <repository changeset_revision="028671f26917" name="package_phemost_1_0" owner="ulfschaefer" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    </package>
+</tool_dependency>