diff mordred_descriptors.xml @ 0:ea68b86303e2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mordred_descriptors.xml	Thu May 23 18:31:43 2019 -0400
@@ -0,0 +1,67 @@
+<tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="0.1.0">
+    <description>with Mordred</description>
+    <requirements>
+        <requirement type="package" version="1.1.2">mordred</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/mordred_descriptors.py'
+            -i '${input}'
+            --iformat '${input.ext}' 
+            -o '${output}'
+            $header
+            $use_3d
+    ]]></command>
+    <inputs>
+        <param name="input" format="smi,sdf,inchi" type="data" label="Molecule data"
+            help="SDF, SMILES or InChi format"/>
+        <param name='header' type='boolean' truevalue='--header' falsevalue=''
+            label='Include a header line' help='Include names of the descriptors as the first line in the output file'/>
+        <param name='use_3d' type='boolean' truevalue='--3d' falsevalue=''
+            label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype='sdf' value="10mol.sdf" />
+            <param name="header" value="True" />
+            <param name="use_3d" value="True" />
+            <output name="output" ftype='tabular' file="10sdf.tab" />
+        </test>
+        <test>
+            <param name="input" ftype='smi' value="8mol.smi" />
+            <param name="header" value="True" />
+            <param name="use_3d" value="False" />
+            <output name="output" ftype='tabular' file="8smi.tab" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+Calculates up to 1825 molecular descriptors using the Mordred package. A list of all
+descriptors is located here_.
+
+.. _here: https://github.com/simonbray/mordred-descriptors
+
+.. class:: infomark
+
+**Input**
+
+A file containing multiples chemical structures, either in SMILES, InChi or SDF format.
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+A tabular file, in which each column represents a molecular descriptor (1613 in total,
+or 1825 if 3D descriptors are included). Each row describes a single molecule. Empty
+cells indicate that a descriptor could not be calculated for that molecule. Rows which
+are entirely empty most likely indicate a wrongly encoded molecule.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s13321-018-0258-y</citation>
+    </citations>
+</tool>