--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PathoID.xml	Thu Apr 13 16:08:52 2017 -0400
@@ -0,0 +1,73 @@
+<tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0">
+  <description>Pathoscope ID</description>
+<requirements>
+    <requirement type="package" version="2.0.6">pathoscope</requirement>
+</requirements>
+<command> <![CDATA[ln -s '$alignFile' align.sam &&
+  pathoscope ID -alignFile align.sam -fileType $fileType -piPrior $piPrior -thetaPrior $thetaPrior
+  -scoreCutoff $scoreCutoff -emEpsilon $emEpsilon -maxIter $maxIter
+  #unless $updatedAlignFile
+    --noUpdatedAlignFile
+  #end unless
+  #unless $displayCutoff
+    --noDisplayCutoff
+  #end unless
+  #if $outMatrix
+    --outMatrix
+  #end if]]>
+</command>
+<inputs>
+  <param format="sam" name="alignFile" type="data" label="Align File"/>
+  <param name="fileType" type="select" label="Choose file type">
+    <option value="sam">Sam File</option>
+  </param>
+  <param name="thetaPrior" type="integer" value="0"
+    optional="true"
+    help="EM Algorithm Theta Prior equivalent to adding n non-unique reads" label="thetaPrior">
+  </param>
+  <param name="piPrior" type="integer" value="0"
+    optional="true"
+    help="EM Algorithm Pi Prior equivalent to adding n unique reads" label="piPrior">
+  </param>
+  <param name="updatedAlignFile" type="boolean" truevalue="yes" falsevalue="no" checked="on" label="Generate updated align file?"/>
+  <param name="displayCutoff" type="boolean" truevalue="yes" falsevalue="no" checked="on" label="Cutoff display genomes?" help="cutoff display of genomes, even if it is insignificant"/>
+  <param name="outMatrix" type="boolean" truevalue="yes" falsevalue="no" checked="off" label="Output alignment matrix"/>
+  <param name="scoreCutoff" type="float" value="0.01" help="Score Cutoff"/>
+  <param name="emEpsilon" type="float" value="1e-7" help="EM Algorithm Epsilon cutoff"/>
+  <param name="maxIter" type="integer" value="50" help="EM Algorithm maximum iterations"/>
+</inputs>
+<outputs>
+  <data format="tsv" name="tableFile" from_work_dir="pathoid-sam-report.tsv" />
+  <data format="sam" name="realignFile" from_work_dir="updated_align.sam" />
+</outputs>
+
+<tests>
+  <test>
+    <param name="alignFile" value="MAP_3852_align.sam"/>
+    <param name="fileType" value="sam" />
+    <param name="thetaPrior" value="0" />
+    <param name="piPrior" value="0" />
+    <param name="updatedAlignFile" checked="on" />
+    <param name="displayCutoff" checked="on" />
+    <param name="outMatrix" checked="off" />
+    <param name="scoreCutoff" value="0.01" />
+    <param name="emEpsilon" value="1e-7" />
+    <param name="maxIter" value="50" />
+    <output name="tsv" file="pathoid-sam-report.tsv"/>
+    <output name="sam" file="updated_align.sam"/>
+  </test>
+</tests>
+
+<help>
+The PathoID module is the core of the PathoScope pipeline. The key is to identify
+reads with unique alignments and use them to guide the reassignment of reads with ambiguous
+alignments.
+</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>