diff ob_grep.xml @ 0:8d51a2cee5c0 draft default tip

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_grep.xml	Sat May 20 08:38:55 2017 -0400
@@ -0,0 +1,86 @@
+<tool id="_obgrep" name="Compound Search" version="@VERSION@.0">
+    <description>an advanced molecular grep program using SMARTS</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>
+<![CDATA[
+        obgrep
+            $invert_matches
+            #if $n_times:
+                -t $n_times
+            #end if
+            $only_name
+            $full_match
+            $number_of_matches
+            -i "${infile.ext}"
+            "${smarts_pattern}"
+            "${infile}"
+            > "${outfile}"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile_all_types"/>
+        <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
+        <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
+        <param name="n_times" type="integer" value="" min="1" optional="True"
+            label="Print a molecule only if the pattern occurs # times inside the molecule" />
+        <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" />
+        <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern" truevalue="-f" falsevalue="" checked="false" />
+        <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
+    </inputs>
+    <options sanitize="False"/>
+    <outputs>
+        <expand macro="output_like_input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="8_mol.smi"/>
+            <param name="smarts_pattern" value="CO"/>
+            <param name="invert_matches" value="False" />
+            <param name="only_name" value="False" />
+            <param name="full_match" value="False" />
+            <param name="number_of_matches" value="False" />
+            <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
+It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
+
+
+.. _Obgrep: http://openbabel.org/wiki/Obgrep
+.. _here: http://openbabel.org/wiki/SMARTS
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - `SD-Format`_
+| - `SMILES Format`_
+
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Same as input format.
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>