changeset 0:cda22c799d0a draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/opsin.xml	Thu Aug 15 03:37:25 2013 -0400
@@ -0,0 +1,62 @@
+<tool id="ctb_opsin" name="IUPAC name-to-structure" version="0.1">
+    <description>converter (OPSIN)</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="1.4.0">opsin</requirement>
+    </requirements>
+    <command>java -jar \$JAVA_JAR_PATH/opsin-1.4.0-jar-with-dependencies.jar "${radicals}" "${wildcards}" -o$oformat &lt; "${infile}" &gt; "${outfile}" </command>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="EXception:" />
+    </stdio>
+    <inputs>
+        <param format="tabular,text" name="infile" type="data" label="IUPAC names" help="Dataset missing? See TIP below"/>
+        <param name="oformat" type="select" label="Output format">
+            <option value="smi">SMILES</option>
+            <option value="cml">Chemical Markup Language</option>
+            <option value="inchi">InChI</option>
+        </param>
+        <param name='radicals' type='boolean' label='Enables interpretation of radicals' truevalue='--allowRadicals' falsevalue='' />
+        <param name='wildcards' type='boolean' label='Radicals are output as wildcard atoms' truevalue='--wildcardRadicals' falsevalue='' />
+    </inputs>
+    <outputs>
+        <data format="smi" name="outfile">
+            <change_format>
+                <when input="oformat" value="cml" format="cml"/>
+                <when input="oformat" value="inchi" format="inchi"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="iupac_names.txt"/>
+            <param name="oformat" value="smi"/>
+            <output name="outfile" file="opsin_results.smi"/>
+        </test>
+    </tests>
+    <help>
+
+
+.. class:: infomark
+
+**What this tool does**
+
+OPSIN_ is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature.
+
+.. _OPSIN: https://bitbucket.org/dan2097/opsin/overview
+
+-----
+
+.. class:: infomark
+    
+**Cite**
+
+Daniel M Lowe, Peter T Corbett, Peter Murray-Rust, Robert C Glen - `Chemical Name to Structure: OPSIN, an Open Source Solution`_
+
+.. _`Chemical Name to Structure: OPSIN, an Open Source Solution`: http://dx.doi.org/10.1021/ci100384d
+
+
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu Aug 15 03:37:25 2013 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
+    <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iupac_names.txt	Thu Aug 15 03:37:25 2013 -0400
@@ -0,0 +1,4 @@
+acetonitrile
+bla
+foo
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/opsin_results.smi	Thu Aug 15 03:37:25 2013 -0400
@@ -0,0 +1,4 @@
+C(C)#N
+
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Aug 15 03:37:25 2013 -0400
@@ -0,0 +1,17 @@
+<tool_dependency>
+    <package name="opsin" version="1.4.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://bitbucket.org/dan2097/opsin/downloads/opsin-1.4.0-jar-with-dependencies.jar</action>
+               <action type="move_file">
+                    <source>opsin-1.4.0-jar-with-dependencies.jar</source>
+                    <destination>$INSTALL_DIR/jars</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Opsin requires a JAVA (1.5+) runtime evironment.</readme>
+    </package>
+</tool_dependency>