# HG changeset patch
# User jasper
# Date 1485284986 18000
# Node ID 2040cda75d1fb1744661eb7784a5dc89e8f5627b

Uploaded

diff -r 000000000000 -r 2040cda75d1f cluster-picker.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster-picker.xml	Tue Jan 24 14:09:46 2017 -0500
@@ -0,0 +1,54 @@
+<tool id="cluster-pick" name="Cluster Picker" version="1.2.3">
+  <description>cluster picker</description>
+<requirements>
+    <requirement type="package" version="1.2.3">cluster-picker</requirement>
+</requirements>
+<!-- <command> <![CDATA[cluster-picker sequence_file tree_file init_threshold main_threshold dis_threshold size genetic_distance]]> </command> -->
+<command> <![CDATA[cluster-picker]]> </command>
+<inputs>
+  <param format="fasta" name="sequence_file" type="data" label="align"
+    help="Please enter fasta format sequences file name to process"/>
+  <param format="nwk" name="tree_file" type="data" label="tree"
+    help="Please enter newick format tree, with branch lengths and node support"/>
+  <param name="init_threshold" type="float" value="0.9" optional="true"
+    help="Please enter initial support threshold for these initial subtrees" label="initial threshold">
+  </param>
+  <param name="main_threshold" type="float" value="0.9" optional="true"
+    help="Please enter main support threshold for clusters" label="main threshold">
+  </param>
+  <param name="dis_threshold" type="float" value="0.045" optional="true"
+    help="Please enter genetic distance threshold for clusters in %" label="distance threshold">
+  </param>
+  <param name="size" type="float" value="10" optional="true"
+    help="To output all cluster names for clusters of size >= X enter X" label="size">
+  </param>
+  <param name="genetic_distance" type="select" label="genetic distance"
+    help="Please enter scoring type for genetic distance\n
+          abs      	= count absolute character differences\n
+          gap      	= disregard sites with -, ~, or n\n
+          valid    	= only count differences for sites with nucleotides: a, c, t, g in both sequences\n
+          ambiguity	= disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)">
+      <option value="gap">gap</option>
+      <option value="abs">abs</option>
+      <option value="valid">valid</option>
+      <option value="ambiguity">ambiguity</option>
+  </param>
+</inputs>
+<outputs>
+  <data format="figTree"/>
+  <data format="nhx"/>
+  <data format="txt"/>
+  <data format="fasta"/>
+</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>
+Cluster identification strategies differ between studies and as a consequence cluster definitions vary.
+</help>
+</tool>