diff ob_addh.xml @ 0:ada6daa717d2 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_addh.xml	Sat May 20 08:37:26 2017 -0400
@@ -0,0 +1,80 @@
+<tool id="openbabel_addh" name="Add hydrogen atoms" version="@VERSION@.0">
+    <description>at a certain pH value</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[
+        python $__tool_directory__/ob_addh.py
+            -i "${infile}"
+            --iformat "${infile.ext}"
+            -o "${outfile}"
+            $polar
+            --pH "${pH_value}"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile_all_types"/>
+        <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
+        <param name="pH_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
+    </inputs>
+    <outputs>
+        <expand macro="output_like_input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="CID_2244.can" ftype="smi" />
+            <param name="polar" value="--polar" />
+            <param name="pH_value" value="7.4" />
+            <output name="outfile" file="CID_2244_addh.can" ftype="smi" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
+
+* Protocol::
+
+	1. The hydrogen atoms included in the input molecule are deleted.
+	2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+3D format files are required, e.g. SDF_
+
+.. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Same output format as the input format.
+
+
+]]>
+    </help>
+    <expand macro="citations">
+        <citation type="doi">10.1186/1752-153X-2-5</citation>
+    </expand>
+</tool>