# HG changeset patch
# User jasper
# Date 1483922368 18000
# Node ID 3fc482539c36b649eb542f988207fc65f5bd5932

Uploaded

diff -r 000000000000 -r 3fc482539c36 PathID.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PathID.xml	Sun Jan 08 19:39:28 2017 -0500
@@ -0,0 +1,51 @@
+<tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0">
+  <description>Pathoscioe ID</description>
+<requirements>
+    <requirement type="package">pathoscope</requirement>
+</requirements>
+<command interpreter="python">pathoscope2.py ID -alignFile $aligh_file -expTag 3852 -tableFile $tableFile
+  -thetaPrior $thetaPrior -piPrior $piPrior --noUpdatedAlignFile $updatedAlignFile --noDisplayCutoff $displayCutoff
+  -scoreCutoff $scoreCutoff -reAlignFile $realignFile </command>
+  <inputs>
+    <param format="sam" name="aligh_file" type="data" label="Align File"/>
+    <param name="file_type" type="select" label="Choose file type">
+      <option value="Sam">Sam File</option>
+    </param>
+    <param argument="--thetaPrior" type="integer" value="0"
+      optional="true"
+      help="EM Algorithm Theta Prior equivalent to adding n non-unique reads" label="thetaPrior">
+    </param>
+    <param argument="--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="select" label="Generate updated align file?">
+        <option value="">No</option>
+        <option value="Yes">Yes</option>
+    </param>
+      <param name="displayCutoff" type="select" label="Cutoff display genomes?" value="Yes" help="cutoff display of genomes, even if it is
+                          insignificant">
+          <option value="">No</option>
+          <option value="Yes">Yes</option>
+      </param>
+      <param name="scoreCutoff" type="integer" value="0" help="Score Cutoff"/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="tableFile" />
+    <data format="sam" name="realignFile" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file1" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>
+
+  <help>
+Reassigns ambiguous reads, identifies microbial strains
+present in the sample, and estimates proportions of
+reads from each genome.
+  </help>
+
+</tool>