# HG changeset patch
# User jasper
# Date 1492712690 14400
# Node ID 07043519e5fdc9f6a343641de37e815171815a02

Uploaded

diff -r 000000000000 -r 07043519e5fd PathoMap.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PathoMap.xml	Thu Apr 20 14:24:50 2017 -0400
@@ -0,0 +1,62 @@
+<tool id="pathoscope_map" name="Pathoscope Map" version="0.1.0">
+  <description> Pathoscope Map </description>
+  <requirements>
+    <requirement type="package" version="2.0.6"> pathoscope </requirement>
+  </requirements>
+  <command> <![CDATA[
+    pathoscope MAP
+    #if str($library.type) == "single"
+      -U $fastqU
+    #elif str($library.type) == "paired"
+      -1 $fastq1
+      -2 $fastq2
+    #end if
+    -indexDir $targetAlignPrefixes.fields.path
+    -targetAlignPrefixes $targetAlignPrefixes
+    -filterAlignPrefixes $filterAlignPrefixes
+    ]]>
+  </command>
+  <inputs>
+    <conditional name="library">
+      <param name="type" type="select" label="Is this single or paired library" help="">
+        <option value="single">Single-end</option>
+        <option value="paired">Paired-end</option>
+      </param>
+      <when value="single">
+        <param name="fastqU" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
+      </when>
+      <when value="paired">
+        <param name="fastq1" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
+        <param name="fastq2" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
+      </when>
+    </conditional>
+    <param name="targetAlignPrefixes" type="select" label="targetAlignPrefixes" help="Target Index Prefixes">
+        <options from_data_table="pathoscope_indexes">
+          <column name="value" index="0"/>
+          <column name="name" index="0"/>
+          <column name="path" index="0"/>
+        </options>
+    </param>
+    <param name="filterAlignPrefixes" type="select" label="filterAlignPrefixes" help="Filter Alignment Files Prefixes">
+      <options from_data_table="pathoscope_indexes">
+        <column name="value" index="0"/>
+        <column name="name" index="0"/>
+        <column name="path" index="0"/>
+      </options>
+    </param>
+  </inputs>
+  <outputs>
+  </outputs>
+  <help>
+    This module will take your reads and map them against a target library. Then it will map the mapping reads
+against a filter library. All the reads that map to the filter library with a score equal or greater than the mapping
+score to the target library will be discarded. The reads mapping with a better score to the target library will be
+used downstream by the PathoID module.
+  </help>
+  <citations>
+    <citation type="doi">10.1101/gr.150151.112</citation>
+    <citation type="doi">10.1186/2049-2618-2-33</citation>
+    <citation type="doi">10.1186/1471-2105-15-262</citation>
+    <citation type="doi">10.4137/CIN.S13890</citation>
+  </citations>
+</tool>