diff ob_remSmall.xml @ 0:2704d4017b13 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_remSmall.xml	Sat May 20 08:39:53 2017 -0400
@@ -0,0 +1,64 @@
+<tool id="openbabel_remSmall" name="Remove small molecules" version="@VERSION@.0">
+    <description></description>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive">
+<![CDATA[
+    obabel
+      -i"${infile.ext}"
+      '${infile}'
+      -ocopy
+      -O '${outfile}'
+      --filter "atoms > $cutoff"
+      -e
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile_all_types"/>
+        <param name="cutoff" type="integer" value="5"
+            label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" />
+    </inputs>
+    <outputs>
+        <expand macro="output_like_input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="3_mol.smi" />
+            <param name="cutoff" value="5" />
+            <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Filters a library of compounds and removes small molecules below a predefined input number of atoms.
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+Some libraries may contain molecules without a 1D/3D descriptor. These molecules may provoke crashes of any other tool. It is strongly adviced to run this tool before proceeding to any further steps.
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Same as input format.
+
+
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>