Mercurial > repos > bgruening > fpocket

diff 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
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line diff
--- a/fpocket.xml	Mon Aug 12 13:27:10 2019 -0400
+++ b/fpocket.xml	Tue Mar 17 12:59:53 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fpocket" name="fpocket" version="0.1.0">
+<tool id="fpocket" name="fpocket" version="3.1.3">
     <description>- find potential binding sites in protein structures</description>
     <requirements>
         <requirement type="package" version="3.1.3">fpocket</requirement>
@@ -49,7 +49,8 @@
         <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output files">
             <option value="atoms" selected="true">PDB files containing the atoms in contact with each pocket</option>
             <option value="pock_verts">PQR files containing Voronoi vertices of each pocket</option>
-            <option value="all_verts">PQR file containing all Voronoi vertices found</option>
+            <option value="alpha_pdb" selected="true">PDB file containing alpha spheres found</option>
+            <option value="all_verts" selected="true">PQR file containing all Voronoi vertices found</option>
             <option value="info" selected="true">Log file containing pocket properties</option>
         </param>
     </inputs>
@@ -66,6 +67,9 @@
         <data format="pqr" name="all_verts_output" label="All Voronoi vertices found" from_work_dir="input_out/input_pockets.pqr">
             <filter>"all_verts" in outputs</filter>
         </data>
+        <data format="pdb" name="alpha_pdb_output" label="PDB output with alpha spheres" from_work_dir="input_out/input_out.pdb">
+            <filter>"alpha_pdb" in outputs</filter>
+        </data>
         <data format="txt" name="info_output" label="Pocket properties" from_work_dir="input_out/input_info.txt">
             <filter>"info" in outputs</filter>
         </data>
@@ -95,6 +99,12 @@
                 <element name="pocket1" ftype="pdb" file="pocket1_atm.pdb" lines_diff="2"/>
             </output_collection>
             <output name="info_output" ftype="txt" file='2brc_info.txt' lines_diff="20"/>
+            <output name="alpha_pdb_output" ftype="pdb">
+              <assert_contents>
+                <has_text text="ATOM      1    N MET A   1"/>
+                <has_text text="HETATM    6 APOL STP C   "/>
+              </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[