diff ob_remIons.xml @ 0:c9bee3591df9 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ob_remIons.xml	Sat May 20 08:39:34 2017 -0400
@@ -0,0 +1,51 @@
+<tool id="openbabel_remIons" name="Remove counterions and fragments" version="@VERSION@.0">
+    <description></description>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive">
+<![CDATA[
+    python '$__tool_directory__/ob_remIons.py'
+      -i '${infile}'
+      -iformat '${infile.ext}'
+      -o '${outfile}'
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile_all_types"/>
+    </inputs>
+    <outputs>
+        <expand macro="output_like_input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="2_mol.smi"/>
+            <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Parses a multiple molecules file and deletes any present counterions or fragments.
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+| Only the **largest fragment** on every molecule is extracted.
+|
+| Only molecules with more than 5 heavy atoms are parsed.
+
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>