diff ob_filter.xml @ 0:0d6e836460be draft

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_filter.xml	Sat May 20 08:38:22 2017 -0400
@@ -0,0 +1,232 @@
+<tool id="openbabel_filter" name="Filter" version="@VERSION@.0">
+    <description> a set of molecules from a file</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 detect_errors="aggressive">
+<![CDATA[
+    python '$__tool_directory__/ob_filter.py'
+      -i '${infile}'
+      -o '${outfile}'
+      -iformat "${infile.ext}"
+      -oformat "${infile.ext}"
+      --filters '{
+        #if $filter_methods.filter_methods_opts == "ruleof5":
+          "hbd" : [0, 5],
+          "hba" : [0, 10],
+          "molwt" : [0, 500],
+          "logp" : [-5, 5],
+        #elif $filter_methods.filter_methods_opts == "LeadLike":
+          "rotbonds" : [0, 7],
+          "molwt" : [0, 350],
+          "logp" : [-5, 3.5],
+        #elif $filter_methods.filter_methods_opts == "DrugLike":
+          "hba" : [0, 10],
+          "rotbonds" : [0, 8],
+          "molwt" : [150, 500],
+          "logp" : [-5, 5],
+          "psa" : [0, 150],
+        #elif $filter_methods.filter_methods_opts == "FragmentLike":
+          "rotbonds" : [0, 5],
+          "molwt" : [0, 250],
+          "logp" : [-5, 2.5],
+        #else:
+          #for $filter in $filter_methods.filter_set:
+            #set $filter_selected = $filter.filter_sel.filter_sel_opts
+            #set $filter_min = $filter_selected + "_min"
+            #set $filter_max = $filter_selected + "_max"
+            "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
+          #end for
+        #end if
+      }'
+]]>
+  </command>
+  <inputs>
+    <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
+        label="Select input file previously annotated with the 'Compute physico-chemical properties' tool"/>
+    <conditional name="filter_methods">
+      <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
+        <option value="user">User-defined properties</option>
+        <option value="ruleof5">Lipinski's Rule-of-Five</option>
+        <option value="LeadLike">Lead-like properties</option>
+        <option value="DrugLike">Drug-like properties</option>
+        <option value="FragmentLike">Fragment-like properties</option>
+      </param>
+      <when value="ruleof5" />
+      <when value="LeadLike" />
+      <when value="DrugLike" />
+      <when value="FragmentLike" />
+      <when value="user">
+        <repeat name="filter_set" title="Filters selection">
+          <conditional name="filter_sel">
+            <param name="filter_sel_opts" type="select" label="Select properties to filter">
+              <option value="hbd">Number of Hydrogen-bond donor groups</option>
+              <option value="hba">Number of Hydrogen-bond acceptor groups</option>
+              <option value="psa">Total polar Surface Area</option>
+              <option value="rotbonds">Number of rotatable bonds</option>
+              <option value="molwt">Molecular weight</option>
+              <option value="logp">Predicted value of LogP</option>
+              <option value="mr">Predicted value for the Molecular Refractivity</option>
+              <option value="atoms">Number of atoms</option>
+              <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
+              <option value="hatoms">Number of heavy atoms</option>-->
+              <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html -->
+              <!--<option value="rings">Number of rings</option>-->
+            </param>
+            <when value="hbd">
+              <param name="hbd_min" type="integer" value="" label="Minimum number of HB donors"/>
+              <param name="hbd_max" type="integer" value="" label="Maximum number of HB donors"/>
+            </when>
+            <when value="hba">
+              <param name="hba_min" type="integer" value="" label="Minimum number of HB acceptors"/>
+              <param name="hba_max" type="integer" value="" label="Maximum number of HB acceptors"/>
+            </when>
+            <when value="psa">
+              <param name="psa_min" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/>
+              <param name="psa_max" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/>
+            </when>
+            <when value="rotbonds">
+              <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/>
+              <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/>
+            </when>
+            <when value="molwt">
+              <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/>
+              <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/>
+            </when>
+            <when value="logp">
+              <param name="logp_min" type="float" value="" label="Minimum threshold value for the log-P"/>
+              <param name="logp_max" type="float" value="" label="Maximum threshold value for the log-P"/>
+            </when>
+            <when value="mr">
+              <param name="mr_min" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/>
+              <param name="mr_max" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/>
+            </when>
+            <when value="atoms">
+              <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
+              <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
+            </when>
+            <!--<when value="rings">
+              <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
+              <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
+            </when>-->
+          </conditional>
+        </repeat>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+        <expand macro="output_like_input"/>
+  </outputs>
+  <tests>
+    <test>
+        <param name="infile" ftype="smi" value="CID_2244.smi"/>
+        <param name="filter_methods_opts" value="ruleof5" />
+        <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
+    </test>
+    <!--
+    Limitation of the test framework:
+    https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820
+    <test>
+        <param name="infile" ftype="smi" value="CID_2244.smi"/>
+        <param name="filter_methods_opts" value="user" />
+        <param name="filter_sel_opts" value="hba" />
+        <param name="hbd_min" value="0" />
+        <param name="hbd_max" value="5" />
+        <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" />
+    </test>
+    -->
+  </tests>
+  <help>
+<![CDATA[
+
+
+.. class:: infomark
+
+**What this tool does**
+
+Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries.
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file.
+|
+| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
+|
+| Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).
+
+-----
+
+.. class:: infomark
+
+**Definition of the pre-defined filtering rules**
+
+  **# Lipinski's Rule of Five:**
+    =< 5 Hydrogen-bond donor groups
+
+    =< 10 Hydrogen-bond acceptor groups
+
+    =< 500 Molecular weight
+
+    =< 5 octanol/water partition coefficient (log P)
+
+  **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
+    =< 7 rotatable bonds
+
+    =< 350 Molecular weight
+
+    =< 3.5 octanol/water partition coefficient (log P)
+
+  **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
+    =< 10 Hydrogen-bond acceptor groups
+
+    =< 8 rotatable bonds
+
+    150 =< Molecular weight =< 500
+
+    =< 150 Polar Surface Area
+
+    =< 5 octanol/water partition coefficient (log P)
+
+  **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
+    =< 5 rotatable bonds
+
+    =< 250 Molecular weight
+
+    =< 2.5 octanol/water partition coefficient (log P)
+
+-----
+
+.. 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**
+
+| SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
+|
+| SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
+
+
+
+]]>
+    </help>
+    <expand macro="citations">
+        <citation type="doi">10.1186/1752-153X-2-5</citation>
+    </expand>
+</tool>