diff chembl.xml @ 0:915e9be38994 draft

planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 2e3c3c2bd7ecdc9c2968a32f91e81136e0cb3835

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chembl.xml	Mon Aug 05 05:21:58 2019 -0400
@@ -0,0 +1,118 @@
+<tool id="chembl" name="Search ChEMBL database" version="0.1.0">
+    <description>for compounds which are similar to a SMILES string</description>
+    <requirements>
+        <requirement type="package" version="0.9.31">chembl_webresource_client</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -W ignore '$__tool_directory__/chembl.py'
+            $input.format '$input.smiles'
+            -o $outfile
+            $search.type
+            #if $search.type == '-t':
+                $search.tanimoto
+            #end if
+            $drugs
+            $biotherapeutic
+            $natprod
+            $ro5
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name='format' type='select' format='text' label="SMILES input type" help="Enter SMILES as either text or file.">
+                <option value='-i'>Text</option>
+                <option value='-f'>File</option>
+            </param>
+            <when value='-i'>
+                <param name="smiles" type="text" label="SMILES input" help="Enter SMILES for a compound.">
+                    <validator type='length' min='5'/>
+                </param>
+            </when>
+            <when value='-f'>
+                <param name="smiles" type="data" format="smi" label="Input file" help="File containing a single compound in SMILES format. Note only the first line of the file will be read, if the file contains multiple compounds."/>
+            </when>
+        </conditional>
+        
+        <conditional name="search">
+            <param name='type' type='select' format='text' label="Search type" help="Search for compounds are similar to the SMILES input, or which contain the SMILES input as a substructure">
+                <option value='-t'>Similarity</option>
+                <option value='-s'>Substructure</option>
+            </param>
+            <when value="-t">
+                <param type="integer" name="tanimoto" label="Tanimoto cutoff score" help="Score for similarity search. Minimum value is 70." value="70" min="70" max="100"/>
+            </when>
+            <when value="-s"/>
+        </conditional>
+        
+        <param name="drugs" type="boolean" value="false" label="Filter to return only approved drugs" truevalue="-d" falsevalue=""/>
+        <param name="biotherapeutic" type="boolean" value="false" label="Filter to return only biotherapeutic molecules" truevalue="-b" falsevalue=""/>
+        <param name="natprod" type="boolean" value="false" label="Filter to return only natural products" truevalue="-n" falsevalue=""/>
+        <param name="ro5" type="boolean" value="false" label="Filter for Lipinski's Rule of Five" truevalue="-r" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="smi" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="format" value="-f"/>
+            <param name="smiles" value="in1.smi"/>
+            <param name='type' value='-t' />
+            <param name='tanimoto' value='70' />
+            <output name="outfile" ftype="smi" file='out1.smi'/>
+        </test>
+        <test>
+            <param name="format" value="-f"/>
+            <param name="smiles" value="in1.smi"/>
+            <param name='type' value='-t' />
+            <param name='tanimoto' value='70' />
+            <param name='drugs' value='true'/>
+            <output name="outfile" ftype="smi" file='out2.smi'/>
+        </test>
+        <test>
+            <param name="format" value="-f"/>
+            <param name="smiles" value="in1.smi"/>
+            <param name='type' value='-s' />
+            <output name="outfile" ftype="smi" file='out3.smi'/>
+        </test>    
+        <test>
+            <param name="format" value="-i"/>
+            <param name="smiles" value="C1CCCCC1"/>
+            <param name='type' value='-t' />
+            <param name='tanimoto' value='70' />
+            <output name="outfile" ftype="smi" file='out4.smi'/>
+        </test>       
+    </tests>
+    <help><![CDATA[
+
+Search the ChEMBL database for compounds which resemble a SMILES string. Two 
+search options are possible: similarity (searches for compounds which are 
+similar to the input within a specified Tanimoto cutoff) and substructure 
+(searches for compounds which contain the input substructure).
+
+Results can be filtered for compounds which are 1) approved drugs 2) biotherapeutic
+3) natural products and 4) fulfil all of the Lipinski rule of five criteria.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+A single molecule in SMILES format. This can be submitted either as text or as a 
+file containing the SMILES string on the first line. Note that if the file contains 
+multiple lines, only the SMILES string on the first line will be used for the search.
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+A SMILES file with search results, each on a new line.
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/nar/gkv352</citation>
+        <citation type="doi">arXiv:1607.00378v1</citation>
+    </citations>
+</tool>