annotate antechamber.xml @ 12:4fff93efc0f9 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 27e76b3f6ed12955fd60609aad4043bc9c60cba2"
author chemteam
date Thu, 07 Oct 2021 09:51:06 +0000
parents e4de81eea04c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
e4de81eea04c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
parents: 2
diff changeset
1 <tool id="ambertools_antechamber" name="AnteChamber" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
2 <description>- Amber's molecular input file processor</description>
0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
3 <macros>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
4 <import>macros.xml</import>
6
e4de81eea04c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
parents: 2
diff changeset
5 <token name="@GALAXY_VERSION@">0</token>
0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
6 </macros>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
7 <expand macro="requirements"></expand>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
8 <command detect_errors="exit_code">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
9 <![CDATA[
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
10 antechamber -i '$input1'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
11 -o '$output1'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
12 -fi '$input1.ext'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
13 -fo '$selected_output_format'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
14 -c '$allparams.c'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
15 -pf '$extraparams.pf'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
16 #if '$extraparams.usenc'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
17 -nc '$allparams.nc'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
18 #end if
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
19 -at '$allparams.at'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
20 -j '$allparams.j'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
21 -rn '$allparams.resname'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
22 -m '$allparams.m'
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
23 ]]>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
24 </command>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
25 <inputs>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
26 <param type="data" name="input1" label="Molecular input (PDB or mol2)" format="pdb,mol2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
27 <param name="selected_output_format" type="select" label="Select an output file format (mol2 recommended!):">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
28 <option value="pdb">pdb</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
29 <option value="mol2" selected="true">mol2</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
30 </param>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
31 <section name="allparams" title="General Parameters" expanded="true">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
32 <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)"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
33 <param name="m" type="integer" value="1" label="Multiplicity" min="1" max="10" help="Multiplicity, 2S+1. Default is 1. (-m)"/>
2
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
34 <param name="resname" type="text" value="MOL" label="Residue name" help="From 1-3 characters allowed. Default is MOL. (-rn)">
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
35 <validator type="regex" message="Maximum of 3 characters allowed.">^[a-zA-Z0-9]{1,3}$</validator>
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
36 </param>
0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
37 <param name="c" type="select" label="Charge method" help="Charge method to use for the calculations. AM1-BCC or RESP recommended (-c)">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
38 <option value="resp">RESP</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
39 <option selected="True" value="bcc">AM1-BCC</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
40 <option value="cm1">CM1</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
41 <option value="cm2">CM2</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
42 <option value="esp">ESP (Kollman)</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
43 <option value="mul">Mulliken</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
44 <option value="gas">Gasteiger</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
45 </param>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
46 <param name="at" type="select" label="Atom type" help="Create atom type for the specified forcefield (-at)">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
47 <option selected="True" value="gaff">gaff</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
48 <option value="gaff2">gaff2</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
49 <option value="amber">amber for PARM94/99/99SB</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
50 <option value="bcc">bcc</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
51 <option value="sybyl">sybyl</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
52 </param>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
53 <param name="j" type="select" label="Atom type and bond type prediction index" help="Specify how to run predictions (-j)">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
54 <option value="0">0 - No assignment</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
55 <option value="1">1 - atom type</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
56 <option value="2">2 - full bond types</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
57 <option value="3">3 - part bond types</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
58 <option selected="True" value="4">4 - atom and full bond type (default)</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
59 <option value="5">5 - atom and part bond type</option>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
60 </param>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
61 </section>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
62 <section name="extraparams" title="Additional Parameters" expanded="false">
2
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
63 <param name="pf" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Remove intermediate files (recommended)" help="(-pf)"/>
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
64 <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."/>
0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
65 </section>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
66 </inputs>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
67 <outputs>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
68 <data format="mol2" name="output1" label="${tool.name}: structure output">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
69 <change_format>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
70 <when input="selected_output_format" value="pdb" format="pdb"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
71 <when input="selected_output_format" value="mol2" format="mol2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
72 <!-- <when input="selected_format" value="xyz" format="xyz"/> <when input="selected_format" value="tinker" format="tinker"/> <when input="selected_format" value="moldy" format="moldy"/> -->
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
73 </change_format>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
74 </data>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
75 </outputs>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
76 <tests>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
77 <test>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
78 <param name="input1" value="LigA.mol2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
79 <section name="allparams">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
80 <param name="nc" value="-2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
81 <param name="c" value="AM1-BCC"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
82 <param name="at" value="gaff2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
83 <param name="j" value="5 - atom and part bond type"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
84 </section>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
85 <output name="output1" file="LigA_output.mol2" compare="diff" lines_diff="0">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
86 <assert_contents>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
87 <has_text text=" 1 C 49.2110 26.9920 85.5530 c2 1 MOL"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
88 </assert_contents>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
89 </output>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
90 </test>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
91 <test>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
92 <param name="input1" value="LigA.pdb" ftype="pdb"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
93 <param name="selected_output_format" value="pdb"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
94 <section name="allparams">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
95 <param name="nc" value="-2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
96 <param name="c" value="AM1-BCC"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
97 <param name="at" value="gaff2"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
98 <param name="j" value="5 - atom and part bond type"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
99 </section>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
100 <output name="output1" file="LigA_output.pdb" compare="diff" lines_diff="0">
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
101 <assert_contents>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
102 <has_text text="ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
103 </assert_contents>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
104 </output>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
105 </test>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
106 </tests>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
107 <help>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
108 <![CDATA[
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
109 .. class:: infomark
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
110
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
111 **What it does**
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
112
2
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
113 Antechamber sets up Amber parameters for the input molecules provided.
0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
114
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
115 .. class:: infomark
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
116
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
117 **How it works**
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
118
2
59a0424937cc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
diff changeset
119 - Select an input file (mol2, PDB)
0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
120 - Specify the correct charge, or keep the default charge of 0
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
121 - Adjust other parameters as needed.
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
122 - Click on Execute
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
123
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
124 .. class:: infomark
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
125
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
126 **Outputs created**
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
127
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
128 - A mol2 or PDB output is created with the forcefield compatible atom names.
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
129
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
130 .. class:: infomark
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
131
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
132 **User guide and documentation**
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
133
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
134 - AmberTools `userguide`_
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
135
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
136
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
137 .. _`userguide`: http://ambermd.org/doc12/Amber19.pdf
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
138
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
139 .. class:: infomark
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
140
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
141 **Feature requests**
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
142
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
143 Go to Galaxy Computational Chemistry and make a `feature request`_
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
144
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
145 .. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
146
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
147
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
148 ]]>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
149 </help>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
150 <expand macro="citations"/>
c01897428864 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
chemteam
parents:
diff changeset
151 </tool>