diff distance_finder.xml @ 0:c066b5accacf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distance_finder.xml	Wed Mar 25 16:47:13 2020 -0400
@@ -0,0 +1,83 @@
+<tool id="openbabel_structure_distance_finder" name="Determine distance to defined points" version="0.1.0">
+    <description>- determine the minimum distances between a molecule and a set of 3D points</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <!-- does not run with obabel 2.4.1 -->
+        <requirement type="package" version="3.0.0">openbabel</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/distance_finder.py'
+            -i '$input'
+            -p $points_file
+            -o '$output'
+    ]]></command>
+
+    <configfiles>
+        <configfile name="points_file">$points</configfile>
+    </configfiles>
+
+    <inputs>
+        <param type="data" name="input" format="sdf" label="Ligands to be analysed" help="Input in SDF format" />
+        <param type="text" name="points" area="true" label="3D points to consider" help="Points as X, Y, Z coordinates, one point per line">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable">
+                    <remove value="&apos;" />
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="sdf" name="output" label="The measured ligands"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="sdf" value="ligands.sdf"/>
+            <!-- TODO - work out how to specify multi-line text -->
+            <param name="points" value="5.655   1.497  18.223" />
+            <output name="output" ftype="sdf">
+                <assert_contents>
+                    <has_text text="distance1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool reports distances of ligands to reference points provided as atoms in a PDB file.
+It is useful for finding out to what extent a ligand occupies an active site.
+
+.. class:: infomark
+
+**Input**
+
+An SD-file containing 3D molecules.
+
+The points parameter contains the points to compare to as X, Y and Z coordinates, one point per line.
+An example  is:
+
+5.655   1.497  18.223
+1.494  -8.367  18.574
+13.034   6.306  25.232
+
+This would encode 3 points.
+
+Each record in the SDF input is read and the closest heavy atom to each of the points is recorded as
+properties in the output SDF.
+
+.. class:: infomark
+
+**Output**
+
+The same SD file as the input but with a series of "distance?" properties added where ? is the index of the points
+being compared to. In the example there would be properties for distance1, distance2 and distance3.
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
+