Mercurial > repos > luis > ball
diff galaxy_stubs/DockPoseClustering.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/DockPoseClustering.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,178 @@ +<?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="DockPoseClustering" name="DockPoseClustering" version="1.1.0"> + <description>clusters docking poses </description> + <macros> + <token name="@EXECUTABLE@">DockPoseClustering</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>DockPoseClustering + +#if $param_i_pdb: + -i_pdb $param_i_pdb +#end if +#if $param_i_dcd: + -i_dcd $param_i_dcd +#end if +#if $param_i_trans: + -i_trans $param_i_trans +#end if +#if $param_o_index_list: + -o_index_list $param_o_index_list +#end if +#if $param_o_score_matrix: + -o_score_matrix $param_o_score_matrix +#end if +#if $param_o_dcd: + -o_dcd $param_o_dcd +#end if +#if $param_rmsd_cutoff: + -rmsd_cutoff $param_rmsd_cutoff +#end if +#if $param_alg: + -alg + #if " " in str($param_alg): + "$param_alg" + #else + $param_alg + #end if +#end if +#if $param_scope: + -scope + #if " " in str($param_scope): + "$param_scope" + #else + $param_scope + #end if +#end if +#if $param_rmsd_type: + -rmsd_type + #if " " in str($param_rmsd_type): + "$param_rmsd_type" + #else + $param_rmsd_type + #end if +#end if +#if $param_o_red_dcd: + -o_red_dcd $param_o_red_dcd +#end if +#if $param_o_cluster_tree: + -o_cluster_tree $param_o_cluster_tree +#end if +#if $param_refine_alg: + -refine_alg + #if " " in str($param_refine_alg): + "$param_refine_alg" + #else + $param_refine_alg + #end if +#end if +#if $param_refine_rmsd_type: + -refine_rmsd_type + #if " " in str($param_refine_rmsd_type): + "$param_refine_rmsd_type" + #else + $param_refine_rmsd_type + #end if +#end if +#if $param_refine_rmsd_scope: + -refine_rmsd_scope + #if " " in str($param_refine_rmsd_scope): + "$param_refine_rmsd_scope" + #else + $param_refine_rmsd_scope + #end if +#end if +#if $param_use_refinement: + -use_refinement $param_use_refinement +#end if +#if $param_run_serial: + -run_serial $param_run_serial +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_o_dcd_id: + -o_dcd_id "$adv_opts.param_o_dcd_id" +#end if + #if $adv_opts.param_o_dcd_dir: + -o_dcd_dir "$adv_opts.param_o_dcd_dir" +#end if +#end if +</command> + <inputs> + <param name="param_i_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb-file" help="(-i_pdb) "/> + <param name="param_i_dcd" type="data" format="dcd" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="input dcd-file" help="(-i_dcd) "/> + <param name="param_i_trans" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="or input transformation file for rigid rmsd clustering" help="(-i_trans) "/> + <param name="param_rmsd_cutoff" type="float" min="0.0" max="100.0" optional="True" value="5.0" label="minimal rmsd between the final clusters (default 5.0)" help="(-rmsd_cutoff) "/> + <param name="param_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for clustering (CLINK_DEFAYS, CLINK_ALTHAUS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-alg) "> + <option value="CLINK_DEFAYS">CLINK_DEFAYS</option> + <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option> + <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option> + <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option> + <option value=" SLINK_SIBSON"> SLINK_SIBSON</option> + </param> + <param name="param_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for scoreing a pose (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-scope) "> + <option value="C_ALPHA">C_ALPHA</option> + <option value=" BACKBONE"> BACKBONE</option> + <option value=" ALL_ATOMS"> ALL_ATOMS</option> + </param> + <param name="param_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for clustering (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-rmsd_type) "> + <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option> + <option value=" RIGID_RMSD"> RIGID_RMSD</option> + <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option> + </param> + <param name="param_refine_alg" type="select" optional="True" value="CLINK_DEFAYS" label="algorithm used for second clustering run (CLINK_DEFAYS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, TRIVIAL_COMPLETE_LINKAGE)" help="(-refine_alg) "> + <option value="CLINK_DEFAYS">CLINK_DEFAYS</option> + <option value=" CLINK_ALTHAUS"> CLINK_ALTHAUS</option> + <option value=" TRIVIAL_COMPLETE_LINKAGE"> TRIVIAL_COMPLETE_LINKAGE</option> + <option value=" NEAREST_NEIGHBOR_CHAIN_WARD"> NEAREST_NEIGHBOR_CHAIN_WARD</option> + <option value=" SLINK_SIBSON"> SLINK_SIBSON</option> + </param> + <param name="param_refine_rmsd_type" type="select" optional="True" value="SNAPSHOT_RMSD" label="rmsd type used for second clustering run (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE)" help="(-refine_rmsd_type) "> + <option value="SNAPSHOT_RMSD">SNAPSHOT_RMSD</option> + <option value=" RIGID_RMSD"> RIGID_RMSD</option> + <option value=" CENTER_OF_MASS_DISTANCE"> CENTER_OF_MASS_DISTANCE</option> + </param> + <param name="param_refine_rmsd_scope" type="select" optional="True" value="C_ALPHA" label="atoms to be considered for rmsd score in second clustering run (C_ALPHA, BACKBONE, ALL_ATOMS)" help="(-refine_rmsd_scope) "> + <option value="C_ALPHA">C_ALPHA</option> + <option value=" BACKBONE"> BACKBONE</option> + <option value=" ALL_ATOMS"> ALL_ATOMS</option> + </param> + <param name="param_use_refinement" type="integer" min="0" max="1" optional="True" value="0" label="Apply a second clustering run with different options (-refine_alg <string>, -refine_rmsd_type <string>, and -refine_rmsd_scope <string>)" help="(-use_refinement) "/> + <param name="param_run_serial" type="integer" min="0" max="1" optional="True" value="0" label="force serial excecution, even if parallel execution would be supported by the algorithm" help="(-run_serial) "/> + <expand macro="advanced_options"> + <param name="param_o_dcd_id" type="text" size="30" value="$o_dcd.id" label="output id" help="(-o_dcd_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_dcd_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last cluster dcd file (if needed)" help="(-o_dcd_dir) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_o_index_list" format="txt"/> + <data name="param_o_score_matrix" format="txt"/> + <data name="param_o_dcd" format="dcd"/> + <data name="param_o_red_dcd" format="dcd"/> + <data name="param_o_cluster_tree" format="dat"/> + </outputs> + <help>This tool computes clusters of docking poses given as conformation set or a list of rigid transformations. + +Parameters are either the input ConformationSet (-i_dcd) and one corresponding pdb file (-i_pdb), or a transformation file (-i_trans). Output can be a cluster index list (-o_index_list), a cluster scoring matrix (-o_score_matrix), or dcd files per cluster (-o_dcd). Optional parameters are the algorithm (-alg), the minimal rmsd between the final clusters (-rmsd_cutoff), the rmsd type (-rmsd_type), and the type of atoms used for scoring a pose (-scope). The optional parameter -o_red_dcd sets the output file for the reduced cluster set (one representative per cluster). The optional parameter -o_cluster_tree specifies the output file for storing the cluster tree. + +Output of this tool depends in the choice of the output parameters. + +</help> +</tool>