diff pbf_ev.xml @ 0:38b8e1d2bb78 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pbf_ev.xml	Tue Jul 21 05:26:38 2020 -0400
@@ -0,0 +1,61 @@
+<tool id="ctb_im_pbf_ev" name="Calculate plane of best fit for molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>using RDKit</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        pbf_ev
+            -i '$infile'
+            -if sdf
+            --meta
+            -of sdf
+            -o outp &>> $logfile &&
+        ##cat outp_metrics.txt &>> $logfile &&
+        gzip -d outp.sdf.gz
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
+    </inputs>
+
+    <expand macro="outputs" />
+
+    <tests>
+        <test>
+            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="Handled 36 molecules, resulting in 36 outputs"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Calculate plane of best fit for molecules.
+
+.. class:: infomark
+
+**Input**
+
+| - Input file in `SDF Format`_
+
+.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SD-file with plane of best fit.
+
+]]></help>
+    <expand macro="citations"/>
+</tool>