--- a/chembl_structure_pipeline.xml	Wed Oct 07 09:31:40 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-<tool id="chembl_structure_pipeline" name="ChEMBL structure pipeline" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
-    <description>for curation and standardizing of molecular structures</description>
-    <macros>
-        <token name="@TOOL_VERSION@">1.0.0</token>
-        <token name="@GALAXY_VERSION@">0</token>
-    </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">chembl_structure_pipeline</requirement>
-    </requirements>  
-    <command><![CDATA[
-        python '$__tool_directory__/structure_pipeline.py' 
-            --input '$input'
-            --output '$output'
-            $standardize
-            $get_parent
-            $check
-]]>
-    </command>
-    <inputs>
-        <param label="SDF/MOL input" type="data" name="input" format="sdf,mol" argument="--input"/>
-        <param label="Standardize" checked="false" type="boolean" name="standardize" argument="--standardize" truevalue="--standardize" falsevalue="" help="Apply the 'Standardize' pipeline component"/>
-        <param label="Get parent" checked="false" type="boolean" name="get_parent" argument="--get_parent" truevalue="--get_parent" falsevalue="" help="Apply the 'GetParent' pipeline component"/>
-        <param label="Check" checked="false" type="boolean" name="check" argument="--check" truevalue="--check" falsevalue="" help="Apply the 'Check' pipeline component"/>
-    </inputs>
-    <outputs>
-        <data name="output" format="sdf" label="Processed molecules"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="o_molblock.mol" />
-            <param name="standardize" value="true" />
-            <output name="output" value="std_molblock.mol"/>
-        </test>
-        <test>
-            <param name="input" value="o_molblock.mol" ftype="mol" />
-            <param name="get_parent" value="true" />
-            <output name="output" value="parent_molblock.mol"/>
-        </test>
-        <test>
-            <param name="input" value="o_molblock.mol" ftype="mol" />
-            <param name="check" value="true" />
-            <output name="output" value="check.mol"/>
-        </test>
-        <test>
-            <param name="input" value="10mol.sdf" ftype="sdf" />
-            <param name="standardize" value="true" />
-            <param name="get_parent" value="true" />
-            <param name="check" value="true" />
-            <output name="output" value="pipeline_multi.sdf"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-
-Apply the ChEMBL chemical curation pipeline to a set of chemical structures in SDF
-format. The pipeline is described in detail in the citation provided (Bento et al.,
-2020).
-
-The pipeline consists of three components:
- - a Standardizer which formats compounds according to defined rules and conventions, based mostly on FDA/IUPAC guidelines.
- - a GetParent component that removes any salts and solvents from the compound to create its parent.
- - a Checker to test the validity of chemical structures and flag any serious errors. Errors are given a code from 0 (least serious) to 10 (most serious), the highest of which is stored in the SDF field `<MaxPenaltyScore>`. A list of all errors encountered is recorded under `<IssueMessages>`.
-
-Either one or more of these protocols can be applied in a single Galaxy job.
-
------
-
-.. class:: infomark
-
-**Input**
-
-One or more molecules in MOL/SDF format.
-
------
-
-.. class:: infomark
-
-**Output**
-
-A MOL/SD-file containing the processed molecules.
-
-]]></help>
-    <citations>
-        <citation type="doi">10.1186/s13321-020-00456-1</citation>
-    </citations>
-</tool>