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comparison fpocket.xml @ 1:909c8763f127 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fpocket/ commit 51f8b6831c513a56bac5aae0d06c936ad6fa8ea8"
author bgruening
date Tue, 17 Mar 2020 12:59:53 -0400
parents 2063e965531c
children 4fb73be7f4cb
comparison
equal deleted inserted replaced
0:2063e965531c 1:909c8763f127
1 <tool id="fpocket" name="fpocket" version="0.1.0"> 1 <tool id="fpocket" name="fpocket" version="3.1.3">
2 <description>- find potential binding sites in protein structures</description> 2 <description>- find potential binding sites in protein structures</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.1.3">fpocket</requirement> 4 <requirement type="package" version="3.1.3">fpocket</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
47 <when value="external"/> 47 <when value="external"/>
48 </conditional> 48 </conditional>
49 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files"> 49 <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
50 <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option> 50 <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
51 <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option> 51 <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
52 <option value="all_verts">PQR file containing all Voronoi vertices found</option> 52 <option value="alpha_pdb" selected="true">PDB file containing alpha spheres found</option>
53 <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option>
53 <option value="info" selected="true">Log file containing pocket properties</option> 54 <option value="info" selected="true">Log file containing pocket properties</option>
54 </param> 55 </param>
55 </inputs> 56 </inputs>
56 57
57 <outputs> 58 <outputs>
63 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_vert\.pqr$" directory="input_out/pockets" ext="pqr"/> 64 <discover_datasets pattern="(?P&lt;designation&gt;^pocket\d+)_vert\.pqr$" directory="input_out/pockets" ext="pqr"/>
64 <filter>"pock_verts" in outputs</filter> 65 <filter>"pock_verts" in outputs</filter>
65 </collection> 66 </collection>
66 <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr"> 67 <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr">
67 <filter>"all_verts" in outputs</filter> 68 <filter>"all_verts" in outputs</filter>
69 </data>
70 <data format="pdb" name="alpha_pdb_output" label="PDB output with alpha spheres" from_work_dir="input_out/input_out.pdb">
71 <filter>"alpha_pdb" in outputs</filter>
68 </data> 72 </data>
69 <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt"> 73 <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt">
70 <filter>"info" in outputs</filter> 74 <filter>"info" in outputs</filter>
71 </data> 75 </data>
72 </outputs> 76 </outputs>
93 <param name='pocket_type' value='small_mol' /> 97 <param name='pocket_type' value='small_mol' />
94 <output_collection name="atoms_output" type="list"> 98 <output_collection name="atoms_output" type="list">
95 <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/> 99 <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/>
96 </output_collection> 100 </output_collection>
97 <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/> 101 <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/>
102 <output name="alpha_pdb_output" ftype="pdb">
103 <assert_contents>
104 <has_text text="ATOM 1 N MET A 1"/>
105 <has_text text="HETATM 6 APOL STP C "/>
106 </assert_contents>
107 </output>
98 </test> 108 </test>
99 </tests> 109 </tests>
100 <help><![CDATA[ 110 <help><![CDATA[
101 111
102 Detect 'pockets' in a protein structure using the fpocket software. A potential use 112 Detect 'pockets' in a protein structure using the fpocket software. A potential use