Mercurial > repos > chemteam > parmconv

annotate parmconv.xml @ 0:1c4b26fe9a88 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
author chemteam
date Tue, 07 Apr 2020 11:53:51 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
1 <tool id="parmconv" name="Convert Parameters" version="@VERSION@">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
2 <description>to AMBER prmtop in preparation for MMPBSA</description>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
3 <macros>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
4 <import>macros.xml</import>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
5 </macros>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
6 <expand macro="requirements">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
7 <requirement type="package" version="3.2.0">parmed</requirement>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
8 <requirement type="package" version="2019.1">gromacs</requirement>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
9 <requirement type="package" version="2.11.1">jinja2</requirement>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
10 </expand>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
11 <command detect_errors="exit_code">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
12 <![CDATA[
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
13 python '$templating_script' '$inputs' &&
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
14 PATH_TO_PARMED=\$(dirname `which parmed`) &&
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
15 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) &&
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
16 export GMXDATA=\$AMBERHOME/share/gromacs/top/ &&
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
17 parmed -i ligand.script -O &&
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
18 parmed -i receptor.script -O &&
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
19 parmed -i complex.script -O &&
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
20 parmed -i solvatedcomplex.script -O
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
21
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
22 ]]>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
23 </command>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
24 <configfiles>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
25 <inputs name="inputs"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
26 <configfile name="templating_script">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
27 <![CDATA[
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
28
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
29 import os
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
30 import sys
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
31 import json
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
32
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
33 from jinja2 import Environment, FileSystemLoader
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
34 input_json_path = sys.argv[1]
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
35 params = json.load(open(input_json_path, "r"))
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
36 currentpath = "$__tool_directory__" # should work generally
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
37 template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
38 template = template_environment.get_template('template_parmconv.j2')
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
39 params['fmt'] = '$param_inputs.fmt'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
40 #if str($param_inputs.fmt) == 'AMBER':
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
41 params["top_in"] = '$param_inputs.top_in'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
42 #else:
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
43 params["top_in"] = '$param_inputs.top_in'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
44 params["str_in"] = '$param_inputs.str_in'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
45 #end if
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
46 params['prmtop_ligand'] = '$prmtop_ligand'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
47 params['prmtop_receptor'] = '$prmtop_receptor'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
48 params['prmtop_complex'] = '$prmtop_complex'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
49 params['prmtop_solvatedcomplex'] = '$prmtop_solvatedcomplex'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
50 print(params)
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
51
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
52
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
53 def unescape(cond_text):
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
54 """
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
55 # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
56 """
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
57 mapped_chars = { '>' :'__gt__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
58 '<' :'__lt__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
59 "'" :'__sq__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
60 '"' :'__dq__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
61 '[' :'__ob__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
62 ']' :'__cb__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
63 '{' :'__oc__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
64 '}' :'__cc__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
65 '@' : '__at__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
66 '\n' : '__cn__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
67 '\r' : '__cr__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
68 '\t' : '__tc__',
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
69 '&' : '__and__'
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
70 }
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
71 for key, value in mapped_chars.items():
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
72 cond_text = cond_text.replace( value, key )
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
73 return cond_text
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
74
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
75 def run_template(params=params, system="ligand"):
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
76 """
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
77 # Render template on a selected system using a local parameter copy
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
78 """
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
79 localparams=params.copy() # shallow copy ok for simple variables
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
80 localparams['stripmask']=unescape(localparams['stripmask_'+system])
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
81 localparams['prmtop_out']=localparams['prmtop_'+system]
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
82 print(localparams)
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
83 with open(system+'.script','w+') as f:
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
84 f.write(template.render(localparams))
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
85
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
86 systems = ['ligand', 'receptor', 'complex', 'solvatedcomplex']
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
87 for system in systems:
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
88 run_template(system=system)
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
89
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
90 ]]>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
91 </configfile>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
92 </configfiles>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
93 <inputs>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
94 <conditional name="param_inputs">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
95 <param name="fmt" type="select" label="Force Field format">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
96 <option selected="True" value="AMBER">AMBER</option>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
97 <option value="GROMACS">GROMACS</option>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
98 </param>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
99 <when value="AMBER">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
100 <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
101 </when>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
102 <when value="GROMACS">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
103 <param name="top_in" type="data" label="Input topology (top) file" format="top"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
104 <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
105 </when>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
106 </conditional>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
107 <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
108 <sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
109 <valid initial="string.printable">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
110 <remove value="&amp;"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
111 </valid>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
112 <mapping initial="none">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
113 <add source="&amp;" target="__and__"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
114 </mapping>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
115 </sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
116 </param>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
117 <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
118 <sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
119 <valid initial="string.printable">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
120 <remove value="&amp;"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
121 </valid>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
122 <mapping initial="none">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
123 <add source="&amp;" target="__and__"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
124 </mapping>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
125 </sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
126 </param>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
127 <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
128 <sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
129 <valid initial="string.printable">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
130 <remove value="&amp;"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
131 </valid>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
132 <mapping initial="none">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
133 <add source="&amp;" target="__and__"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
134 </mapping>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
135 </sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
136 </param>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
137 <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
138 <sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
139 <valid initial="string.printable">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
140 <remove value="&amp;"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
141 </valid>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
142 <mapping initial="none">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
143 <add source="&amp;" target="__and__"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
144 </mapping>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
145 </sanitizer>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
146 </param>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
147 </inputs>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
148 <outputs>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
149 <data format="txt" name="prmtop_ligand" label="ligand prmtop"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
150 <data format="txt" name="prmtop_receptor" label="receptor prmtop"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
151 <data format="txt" name="prmtop_complex" label="complex prmtop"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
152 <data format="txt" name="prmtop_solvatedcomplex" label="solvated complex prmtop"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
153 </outputs>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
154 <tests>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
155 <test>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
156 <!--example in this test is not solvated but sufficient -->
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
157 <param name="fmt" value="AMBER"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
158 <conditional name="param_inputs">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
159 <param name="top_in" value="complex.prmtop"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
160 </conditional>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
161 <param name="stripmask_ligand" value="!:RAL"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
162 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT,RAL"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
163 <param name="stripmask_complex" value=":NA,CL,SOL,WAT"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
164 <output name="prmtop_ligand">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
165 <assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
166 <has_text text=" 61 15"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
167 <has_text text="%FLAG MASS"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
168 <has_text text="RAL"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
169 </assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
170 </output>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
171 <output name="prmtop_receptor">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
172 <assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
173 <has_text text=" 3880 15"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
174 <has_text text="%FLAG MASS"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
175 <has_text text="ALA LEU"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
176 <not_has_text text="RAL "/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
177 </assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
178 </output>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
179 <output name="prmtop_complex">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
180 <assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
181 <has_text text=" 3941 15"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
182 <has_text text="%FLAG MASS"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
183 <has_text text="ALA LEU"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
184 <has_text text="RAL"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
185 </assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
186 </output>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
187 </test>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
188 <test>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
189 <!--example in this test is from @sbrays' gromacs tests. It has no ligand but is sufficient and will not take extra space in the repo! -->
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
190 <param name="fmt" value="GROMACS"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
191 <conditional name="param_inputs">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
192 <param name="top_in" value="topol_solv.top"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
193 <param name="str_in" value="solv_ions.gro"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
194 </conditional>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
195 <!-- pretending CL is a ligand -->
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
196 <param name="stripmask_ligand" value="!:CL"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
197 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
198 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
199 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
200 <output name="prmtop_ligand">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
201 <assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
202 <has_text text=" 8 59"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
203 <has_text text="%FLAG MASS"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
204 <has_text text="CL"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
205 </assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
206 </output>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
207 <output name="prmtop_receptor">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
208 <assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
209 <has_text text=" 1960 59"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
210 <has_text text="%FLAG MASS"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
211 <has_text text="LYS VAL PHE "/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
212 <not_has_text text="CL "/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
213 </assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
214 </output>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
215 <output name="prmtop_solvatedcomplex">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
216 <assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
217 <has_text text=" 38265 59"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
218 <has_text text="%FLAG MASS"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
219 <has_text text="LYS VAL PHE"/>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
220 </assert_contents>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
221 </output>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
222 </test>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
223 </tests>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
224 <help>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
225 <![CDATA[
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
226 .. class:: infomark
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
227
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
228 **What it does**
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
229
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
230 This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMPBSA calculations.
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
231
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
232 .. class:: infomark
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
233
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
234 **How it works**
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
235
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
236 AmberTools ParmEd is used to strip unneeded atoms and save out the parameter files. The stripmasks are defined by the user.
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
237
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
238 .. class:: infomark
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
239
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
240 **Outputs created**
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
241
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
242 prmtop files for the ligand, receptor, complex and solvated complex.
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
243
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
244 .. class:: infomark
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
245
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
246 **User guide and documentation**
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
247
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
248 - The `AmberTools Manual`_
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
249 - The `Parmed Documentation`_
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
250
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
251
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
252 .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
253 .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
254
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
255
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
256 ]]>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
257 </help>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
258 <expand macro="citations">
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
259 <citation type="bibtex">@misc{parmed_2020, author = {ParmEd}, title = {ParmEd/ParmEd}, url={https://github.com/ParmEd/ParmEd}, abstract = {Parameter/topology editor and molecular simulator. Contribute to ParmEd/ParmEd development by creating an
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
260 account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
261 </expand>
1c4b26fe9a88 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
parents:
diff changeset
262 </tool>