diff align-it.xml @ 0:1b8b6787dfbb draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
author bgruening
date Mon, 22 May 2017 03:02:39 -0400
parents
children 10c0df29e6d1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align-it.xml	Mon May 22 03:02:39 2017 -0400
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+<tool id="ctb_alignit" name="Pharmacophore Alignment" version="1.0.3.1">
+    <description>and Optimization (Align-it)</description>
+    <requirements>
+        <requirement type="package" version="1.0.3">align_it</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+<![CDATA[
+        align-it
+            #if str($database.ext).strip() == 'phar':
+                --dbType PHAR
+            #else:
+                --dbType '${database.ext}'
+            #end if
+            --dbase "$database"
+
+            --reference "$reference"
+            #if str($reference.ext).strip() == 'phar':
+                --refType PHAR
+            #else:
+                --refType ${reference.ext}
+            #end if
+            #######################################
+            #### output options
+            #######################################
+            --pharmacophore $aligned_pharmacophores
+
+
+            --out '$aligned_structures'
+            --outType $oformat
+
+            #if float( str($cutoff) ) > 0:
+                --cutOff $cutoff
+            #end if
+            #if int( str($best) ) > 0:
+                --best $best
+            #end if
+            --rankBy $rankBy
+            --scores '$score_result_file'
+
+            #######################################
+            #### Options
+            #######################################
+
+            #set $fgroups_combined = str( $fgroups ).strip()
+            --funcGroup $fgroups_combined
+
+            --epsilon $epsilon
+            $merge
+            $noNormal
+            $noHybrid
+            $scoreOnly
+            $withExclusion
+]]>
+    </command>
+    <inputs>
+        <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/>
+        <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference Molecule"/>
+
+        <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment">
+            <option value='AROM' selected="true">aromatic rings</option>
+            <option value='HDON' selected="true">hydrogen bond donors</option>
+            <option value='HACC' selected="true">hydrogen bond acceptors</option>
+            <option value='LIPO' selected="true">lipophilic spots</option>
+            <option value='CHARGE' selected="true">charge centers</option>
+        </param>
+
+
+        <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase'
+            help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned.">
+            <validator type="in_range" min="0" max="1" />
+        </param>
+        <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
+        <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue='' 
+            label='No normal information is included during the alignment'
+            help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/>
+        <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue=''
+            label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/>
+        <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue=''
+            label='Add exclusion spheres into the optimization process instead of processing them afterwards'
+            help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." />
+        <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue=''
+            label='No translational or rotational optimization will be performed' help=""/>
+
+        <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format">
+            <option value='smi'>SMILES</option>
+            <option value='inchi'>InChI</option>
+            <option value='sdf'>SD file</option>
+        </param>
+
+        <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files"
+            help="This value should be between 0 and 1.">
+            <validator type="in_range" min="0" max="1" />
+        </param>
+        <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files"
+            help="0 means this option is deactivated">
+            <validator type="in_range" min="0"/>
+        </param>
+
+        <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
+            <option value='TANIMOTO'>Tanimoto</option>
+            <option value='TVERSKY_REF'>TVERSKY_REF</option>
+            <option value='TVERSKY_DB'>TVERSKY_DB</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="aligned_pharmacophores" format="txt" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
+        <data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
+            <change_format>
+                <when input="oformat" value="inchi" format="inchi"/>
+                <when input="oformat" value="sdf" format="sdf"/>
+            </change_format>
+        </data>
+        <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="database" ftype="sdf" value="CID_2244.sdf"/>
+            <param name="reference" ftype="sdf" value="CID_2244.sdf"/>
+            <param name="oformat" value="sdf"/>
+            <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" />
+            <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" />
+            <output name="score_result_file" file="aliginit_scores.tabular.tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Align-it_ is a tool to align molecules according to their pharmacophores.
+A pharmacophore is an abstract concept based on the specific interactions
+observed in drug-receptor interactions: hydrogen bonding,
+charge transfer, electrostatic and hydrophobic interactions.
+Molecular modeling and/or screening based on pharmacophore similarities
+has been proven to be an important and useful method in drug discovery.
+
+The functionality of Align-it_ consists mainly of two parts.
+The first functionality is the generation of pharmacophores from molecules
+(use the tool **Pharmacophore generation** if you want to store these for further use).
+Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting
+score is calculated from the volume overlap resulting of the alignments.
+
+.. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+* Example::
+
+    - database
+
+     30 31  0     0  0  0  0  0  0999 V2000
+        1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+        1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+       -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.7906   -1.9108    0.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
+        0.2679   -0.2051   -0.3990 N   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.0640    0.5139   -0.3769 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.7313    0.7178   -0.0192 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.4761   -0.6830   -1.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
+        1.6571   -0.2482   -0.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -3.0382    1.4350    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.3728    1.8429    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.6797    2.5600    0.7506 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.3470    2.7640    1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
+        2.5353    0.3477   -1.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
+        2.1740   -0.8865    0.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.8480   -1.8749   -0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
+        3.9124    0.3058   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
+        3.5511   -0.9285    1.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
+        4.4203   -0.3324    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.7086   -0.9792   -1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -3.3614   -0.4266   -1.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.0861   -1.1146   -0.6780 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -4.0812    1.2885   -0.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.6569    2.0278    1.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -3.4382    3.2769    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.0683    3.6399    1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
+        4.6037    0.7654   -1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
+        3.9635   -1.4215    2.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
+        5.4925   -0.3651    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -3.5025   -3.7011   -0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
+
+    - cutoff : 0.0
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+The format of the output file is shown in the table below:
+
++--------+-----------------------------------------------------------------------+
+| Column |                           Content                                     |
++========+=======================================================================+
+|    1   | Id of the reference structure                                         |
++--------+-----------------------------------------------------------------------+
+|    2   | Maximum volume of the reference structure                             |
++--------+-----------------------------------------------------------------------+
+|    3   | Id of the database structure                                          |
++--------+-----------------------------------------------------------------------+
+|    4   | Maximum volume of the database structure                              |
++--------+-----------------------------------------------------------------------+
+|    5   | Maximum volume overlap of the two structures                          |
++--------+-----------------------------------------------------------------------+
+|    6   | Overlap between pharmacophore and exclusion spheres in the reference  |
++--------+-----------------------------------------------------------------------+
+|    7   | Corrected volume overlap between database pharmacophore and reference |
++--------+-----------------------------------------------------------------------+
+|    8   | Number of pharmacophore points in the processed pharmacophore         |
++--------+-----------------------------------------------------------------------+
+|    9   | TANIMOTO score                                                        |
++--------+-----------------------------------------------------------------------+
+|   10   | TVERSKY_REF score                                                     |
++--------+-----------------------------------------------------------------------+
+|   11   | TVERSKY_DB score                                                      |
++--------+-----------------------------------------------------------------------+
+
+
+* Example::
+
+    - aligned Pharmacophores
+
+        3033
+        HYBL    -1.98494    1.9958    0.532089    0.7    0    0    0    0
+        HYBL    3.52122    -0.309347    0.122783    0.7    0    0    0    0
+        HYBH    -3.262    -2.9284    -1.0647    1    1    -3.5666    -3.7035    -1.61827
+        HDON    0.2679    -0.2051    -0.399    1    1    -0.076102    -0.981133    -0.927616
+        HACC    -2.7906    -1.9108    0.9092    1    1    -2.74368    -1.94015    1.90767
+        $$$$
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jmgm.2008.04.003</citation>
+    </citations>
+</tool>