# HG changeset patch
# User jasper
# Date 1488229046 18000
# Node ID f796c7a7c7b7d13e52a82f33a3fef10035bab0aa
# Parent  c849d1e6ee3ef0c809da26e05d34f219352725b7
Deleted selected files

diff -r c849d1e6ee3e -r f796c7a7c7b7 PathID.xml
--- a/PathID.xml	Tue Jan 10 15:41:33 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-<tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0">
-  <description>Pathoscioe ID</description>
-<requirements>
-    <requirement type="package" version="2.0.6">pathoscope</requirement>
-</requirements>
-<command> <![CDATA[pathoscope -h]]>  </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>