diff get_pubchem_as_smiles.xml @ 0:cd19c3fab3a6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_pubchem_as_smiles.xml	Wed May 22 07:44:03 2019 -0400
@@ -0,0 +1,58 @@
+<tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" version="0.2" >
+    <description>as canonical SMILES</description>
+    <requirements>
+        <requirement type="package" version="2.4.1">openbabel</requirement>
+        <requirement type="package" version="2.7">python</requirement>
+    </requirements>
+    <stdio>
+        <regex match="obError"
+               source="both"
+               level="fatal"
+               description="Critical Open Babel error" />
+        <regex match="obWarning"
+               source="both"
+               level="warning"
+               description="Non-critical Open Babel warning" />
+        <regex match="obInfo"
+               source="both"
+               level="log"
+               description="Open Babel Information" />
+    </stdio>
+    <command>
+<![CDATA[
+        python '$__tool_directory__/get_pubchem_as_smiles.py'
+            -o $pubchem_smi
+            -p \${GALAXY_SLOTS:-4}
+            ## temporary hack until my Galaxy patch is committed
+            > /dev/null 2>&1
+]]>
+    </command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data format="smi" name="pubchem_smi" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.
+
+.. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+The output will be one large SMILES file.
+
+]]>
+    </help>
+</tool>