Mercurial > repos > luis > ball
diff galaxy_stubs/ExtractClustersFromWardTree.xml @ 2:605370bc1def draft default tip
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author | luis |
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date | Tue, 12 Jul 2016 12:33:33 -0400 |
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--- /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="<class 'CTDopts.CTDopts._Null'>" 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="""/> + </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>