# HG changeset patch
# User jasper
# Date 1492713994 14400
# Node ID 3663119f968a8549eb71f2809006c69818f6e4bc
# Parent  07043519e5fdc9f6a343641de37e815171815a02
Deleted selected files

diff -r 07043519e5fd -r 3663119f968a PathoMap.xml
--- a/PathoMap.xml	Thu Apr 20 14:24:50 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-<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>