diff galaxy_stubs/ExtractClustersFromWardTree.xml @ 2:605370bc1def draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/ExtractClustersFromWardTree.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,79 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Docking]-->
+<tool id="ExtractClustersFromWardTree" name="ExtractClustersFromWardTree" version="1.1.0">
+  <description>extracts docking clusters </description>
+  <macros>
+    <token name="@EXECUTABLE@">ExtractClustersFromWardTree</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ExtractClustersFromWardTree
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_i_type:
+  -i_type     "$param_i_type"
+#end if
+#if $param_o_out:
+  -o_out $param_o_out
+#end if
+#if $param_o_type:
+  -o_type
+  #if " " in str($param_o_type):
+    "$param_o_type"
+  #else
+    $param_o_type
+  #end if
+#end if
+#if $param_cutoff_type:
+  -cutoff_type
+  #if " " in str($param_cutoff_type):
+    "$param_cutoff_type"
+  #else
+    $param_cutoff_type
+  #end if
+#end if
+#if $param_cut_value:
+  -cut_value $param_cut_value
+#end if
+#if $param_min_size:
+  -min_size $param_min_size
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="dat" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input serialized cluster file" help="(-i) "/>
+    <param name="param_i_type" type="text" size="30" value="binary" label="input type (binary, text)" help="(-i_type) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_o_type" type="select" optional="True" value="index_list" label="output type (gv, json, index_list)" help="(-o_type) ">
+      <option value="gv">gv</option>
+      <option value=" json"> json</option>
+      <option value=" index_list"> index_list</option>
+    </param>
+    <param name="param_cutoff_type" type="select" optional="True" value="ward_distance" label="cutoff type (ward_distance, num_clusters)" help="(-cutoff_type) ">
+      <option value="ward_distance">ward_distance</option>
+      <option value=" num_clusters"> num_clusters</option>
+    </param>
+    <param name="param_cut_value" type="float" min="0.0" max="10000.0" optional="True" value="5.0" label="cut value for splitting the given WART tree using the cutoff-type (default 5.0)" help="(-cut_value) "/>
+    <param name="param_min_size" type="integer" min="1" max="10000" optional="True" value="1" label="minimal size of clusters (default 1)" help="(-min_size) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o_out" format="gv"/>
+  </outputs>
+  <help>This tool extracts clusters of docking poses given a dat file.
+
+Parameters are the filename (-i) of the serialized cluster tree, the output filename (-o_out), the output type (-o_type). The optional parameter -i_type allows to switch between binary (default) and text file for the cluster tree input, parameter -min_size allows to filter for cluster of a minimal size, parameter -cutoff_type defines the way to cut the cluster tree (either by ward distance or by a target number of clusters) using paramter -cut_value.
+
+Output of this tool is the extracted cluster tree, either as index list, as graph visualization (gv) input, or as json
+
+</help>
+</tool>