diff select_points_SDF.xml @ 0:7a4306d69801 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 6037a8c8d53839daad1b183e1ae0329862ac2c2c"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/select_points_SDF.xml	Mon May 04 07:41:13 2020 -0400
@@ -0,0 +1,62 @@
+<tool id="ctb_frankenstein_ligand" name="Create Frankenstein ligand" version="0.1.0">
+    <description>for docking active site definition</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/select_points_SDF.py'
+            -i '$infile'
+            -o '$outfile'
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
+    </inputs>    
+    <outputs>
+        <data name="outfile" format="sdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="input.sdf" ftype="sdf"/>
+            <output name="outfile" ftype='sdf' file="select_points_output.sdf"/>
+        </test>
+        <test>
+            <param name="infile" value="input_v3000.sdf" ftype="sdf"/>
+            <output name="outfile" ftype='sdf' file="select_points_output_v3000.sdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Converts an SD file containing multiple molecules into a 'Frankenstein ligand' with a 3D shape combining all ligands, which can be used for definition of an active site with rDock.
+
+This tool is based on a Perl script originally written by Peter Schmidtke.
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - SD file containing multiple molecules.
+
+_____
+        
+.. class:: infomark
+
+**Output**
+
+       - SD file containing the 'Frankenstein ligand'.
+    ]]></help>
+       <citations>
+            <citation type="doi">10.1371/journal.pcbi.1003571</citation>
+            <citation type="bibtex">
+            @article{rdock,
+                author = {Peter Schmidtke},
+                title = {'Select points' script for generation of a Frankenstein ligand},
+                url = {https://github.com/InformaticsMatters/docking-validation/blob/master/scripts/select_points_SDF.pl}
+        }</citation>
+       </citations>
+</tool>