--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PathoMap.xml	Sat Apr 22 23:47:18 2017 -0400
@@ -0,0 +1,77 @@
+<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[
+    #from os import listdir
+    #set path=$targetIndexPrefixes.fields.path.split(',')[0]
+    #set prefixes=[f for f in listdir(path) if f.endswith(".3.bt2")]
+    #set targetRefs=str($targetIndexPrefixes)
+    #set targetR=targetRefs.split(',')
+    #set p=[]
+    #for $f in prefixes
+      #for $t in targetR
+        #if $t in f
+          #set p = p + [f[:-6]]
+        #end if
+      #end for
+    #end for
+    #set target=','.join(p)
+    pathoscope MAP
+    #if str($reads.type) == "single"
+      -U $fastqU
+    #elif str($reads.type) == "paired"
+      -1 $fastq1
+      -2 $fastq2
+    #end if
+    -indexDir $path
+    -targetIndexPrefixes $target
+    -filterIndexPrefixes $filterIndexPrefixes 2>&1
+    && mv outalign.sam "$outalign"
+    && mv pathomap-appendAlign.fq "$pathomap_appendAlign"
+    ]]>
+  </command>
+  <inputs>
+    <conditional name="reads">
+      <param name="type" type="select" label="Is this single or paired reads" 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="targetIndexPrefixes" multiple="true" type="select" label="targetIndexPrefixes" help="Target Index Prefixes">
+        <options from_data_table="pathoscope_indexes">
+          <filter type="sort_by" column="2"/>
+          <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+        </options>
+    </param>
+    <param name="filterIndexPrefixes" multiple="true" type="select" label="filterIndexPrefixes" help="Filter Index Prefixes">
+      <options from_data_table="pathoscope_indexes">
+        <filter type="sort_by" column="2"/>
+        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+      </options>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="sam" name="outalign" label="outalign.sam" />
+    <data format="fastqsanger" name="pathomap_appendAlign" label="pathomap_appendAlign.fastq" />
+  </outputs>
+
+  <help>
+  IMPORTANT: The name and the path of the reference database (with bowtie indexed)
+  should be added to the pathoscope.loc entry.
+  </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>