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comparison antechamber.xml @ 2:1fec6d846b48 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:33:48 -0400
parents b2e4247a9f1c
children
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1:72e012c35199 2:1fec6d846b48
1 <tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@"> 1 <tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@">
2 <description>Amber's molecular input file processor</description> 2 <description>- Amber's molecular input file processor</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"></expand>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
28 <option value="mol2" selected="true">mol2</option> 28 <option value="mol2" selected="true">mol2</option>
29 </param> 29 </param>
30 <section name="allparams" title="General Parameters" expanded="true"> 30 <section name="allparams" title="General Parameters" expanded="true">
31 <param name="nc" type="integer" value="0" label="Net charge" min="-50" max="50" help="Specify the net charge for the molecule. Default is 0. (-nc)"/> 31 <param name="nc" type="integer" value="0" label="Net charge" min="-50" max="50" help="Specify the net charge for the molecule. Default is 0. (-nc)"/>
32 <param name="m" type="integer" value="1" label="Multiplicity" min="1" max="10" help="Multiplicity, 2S+1. Default is 1. (-m)"/> 32 <param name="m" type="integer" value="1" label="Multiplicity" min="1" max="10" help="Multiplicity, 2S+1. Default is 1. (-m)"/>
33 <param name="resname" type="text" value="MOL" label="Residue name" help="From 1-3 characters allowed. Default is MOL. (-rn)"/> 33 <param name="resname" type="text" value="MOL" label="Residue name" help="From 1-3 characters allowed. Default is MOL. (-rn)">
34 <validator type="regex" message="Maximum of 3 characters allowed.">^[a-zA-Z0-9]{1,3}$</validator>
35 </param>
34 <param name="c" type="select" label="Charge method" help="Charge method to use for the calculations. AM1-BCC or RESP recommended (-c)"> 36 <param name="c" type="select" label="Charge method" help="Charge method to use for the calculations. AM1-BCC or RESP recommended (-c)">
35 <option value="resp">RESP</option> 37 <option value="resp">RESP</option>
36 <option selected="True" value="bcc">AM1-BCC</option> 38 <option selected="True" value="bcc">AM1-BCC</option>
37 <option value="cm1">CM1</option> 39 <option value="cm1">CM1</option>
38 <option value="cm2">CM2</option> 40 <option value="cm2">CM2</option>
55 <option selected="True" value="4">4 - atom and full bond type (default)</option> 57 <option selected="True" value="4">4 - atom and full bond type (default)</option>
56 <option value="5">5 - atom and part bond type</option> 58 <option value="5">5 - atom and part bond type</option>
57 </param> 59 </param>
58 </section> 60 </section>
59 <section name="extraparams" title="Additional Parameters" expanded="false"> 61 <section name="extraparams" title="Additional Parameters" expanded="false">
60 <param name="pf" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="remove intermediate files (recommended)" help="(-pf)"/> 62 <param name="pf" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Remove intermediate files (recommended)" help="(-pf)"/>
61 <param name="usenc" type="boolean" checked="true" truevalue="True" falsevalue="False" label="use netcharge (recommended)" help="Can choose to let the charge be inferred by setting this to False."/> 63 <param name="usenc" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Use net charge (recommended)" help="Can choose to let the charge be inferred by setting this to False."/>
62 </section> 64 </section>
63 </inputs> 65 </inputs>
64 <outputs> 66 <outputs>
65 <data format="mol2" name="output1" label="${tool.name}: structure output"> 67 <data format="mol2" name="output1" label="${tool.name}: structure output">
66 <change_format> 68 <change_format>
105 <![CDATA[ 107 <![CDATA[
106 .. class:: infomark 108 .. class:: infomark
107 109
108 **What it does** 110 **What it does**
109 111
110 Antechamber sets up parameters for the input molecules provided. 112 Antechamber sets up Amber parameters for the input molecules provided.
111 113
112 .. class:: infomark 114 .. class:: infomark
113 115
114 **How it works** 116 **How it works**
115 117
116 - Select an input file (PDB, mol2) 118 - Select an input file (mol2, PDB)
117 - Specify the correct charge, or keep the default charge of 0 119 - Specify the correct charge, or keep the default charge of 0
118 - Adjust other parameters as needed. 120 - Adjust other parameters as needed.
119 - Click on Execute 121 - Click on Execute
120 122
121 .. class:: infomark 123 .. class:: infomark