Mercurial > repos > chemteam > parmconv
annotate parmconv.xml @ 1:da2252f1ccab draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
author | chemteam |
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date | Mon, 25 Jan 2021 11:15:06 +0000 |
parents | 6c6cecf51bd0 |
children | 2b82fc7bec67 |
rev | line source |
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1
da2252f1ccab
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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1 <tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> |
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6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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2 <description>to AMBER prmtop in preparation for MMPBSA</description> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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3 <macros> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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4 <import>macros.xml</import> |
1
da2252f1ccab
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
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5 <token name="@GALAXY_VERSION@">0</token> |
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6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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6 </macros> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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7 <expand macro="requirements"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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8 <requirement type="package" version="3.2.0">parmed</requirement> |
1
da2252f1ccab
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
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9 <requirement type="package" version="2020.4">gromacs</requirement> |
da2252f1ccab
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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10 <requirement type="package" version="2.11.2">jinja2</requirement> |
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6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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11 </expand> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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12 <command detect_errors="exit_code"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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13 <![CDATA[ |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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14 python '$templating_script' '$inputs' && |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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15 PATH_TO_PARMED=\$(dirname `which parmed`) && |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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16 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) && |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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17 export GMXDATA=\$AMBERHOME/share/gromacs/top/ && |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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18 parmed -i ligand.script -O && |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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19 parmed -i receptor.script -O && |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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20 parmed -i complex.script -O && |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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21 parmed -i solvatedcomplex.script -O |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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22 |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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23 ]]> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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24 </command> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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25 <configfiles> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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26 <inputs name="inputs"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
chemteam
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27 <configfile name="templating_script"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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28 <![CDATA[ |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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29 |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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30 import os |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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31 import sys |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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32 import json |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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33 |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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34 from jinja2 import Environment, FileSystemLoader |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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35 input_json_path = sys.argv[1] |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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36 params = json.load(open(input_json_path, "r")) |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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37 currentpath = "$__tool_directory__" # should work generally |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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38 template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True) |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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39 template = template_environment.get_template('template_parmconv.j2') |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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40 params['fmt'] = '$param_inputs.fmt' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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41 #if str($param_inputs.fmt) == 'AMBER': |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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42 params["top_in"] = '$param_inputs.top_in' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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43 #else: |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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44 params["top_in"] = '$param_inputs.top_in' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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45 params["str_in"] = '$param_inputs.str_in' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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46 #end if |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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47 params['prmtop_ligand'] = '$prmtop_ligand' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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48 params['prmtop_receptor'] = '$prmtop_receptor' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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49 params['prmtop_complex'] = '$prmtop_complex' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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50 params['prmtop_solvatedcomplex'] = '$prmtop_solvatedcomplex' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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51 print(params) |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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52 |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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53 |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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54 def unescape(cond_text): |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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55 """ |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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56 # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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57 """ |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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58 mapped_chars = { '>' :'__gt__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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59 '<' :'__lt__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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60 "'" :'__sq__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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61 '"' :'__dq__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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62 '[' :'__ob__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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63 ']' :'__cb__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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64 '{' :'__oc__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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65 '}' :'__cc__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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66 '@' : '__at__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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67 '\n' : '__cn__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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68 '\r' : '__cr__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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69 '\t' : '__tc__', |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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70 '&' : '__and__' |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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71 } |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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72 for key, value in mapped_chars.items(): |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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73 cond_text = cond_text.replace( value, key ) |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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74 return cond_text |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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75 |
6c6cecf51bd0
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76 def run_template(params=params, system="ligand"): |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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77 """ |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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78 # Render template on a selected system using a local parameter copy |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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79 """ |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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80 localparams=params.copy() # shallow copy ok for simple variables |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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81 localparams['stripmask']=unescape(localparams['stripmask_'+system]) |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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82 localparams['prmtop_out']=localparams['prmtop_'+system] |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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83 print(localparams) |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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84 with open(system+'.script','w+') as f: |
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85 f.write(template.render(localparams)) |
6c6cecf51bd0
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86 |
6c6cecf51bd0
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87 systems = ['ligand', 'receptor', 'complex', 'solvatedcomplex'] |
6c6cecf51bd0
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88 for system in systems: |
6c6cecf51bd0
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89 run_template(system=system) |
6c6cecf51bd0
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90 |
6c6cecf51bd0
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91 ]]> |
6c6cecf51bd0
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92 </configfile> |
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93 </configfiles> |
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94 <inputs> |
6c6cecf51bd0
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95 <conditional name="param_inputs"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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96 <param name="fmt" type="select" label="Force Field format"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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97 <option selected="True" value="AMBER">AMBER</option> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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98 <option value="GROMACS">GROMACS</option> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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99 </param> |
6c6cecf51bd0
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100 <when value="AMBER"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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101 <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/> |
6c6cecf51bd0
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102 </when> |
6c6cecf51bd0
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103 <when value="GROMACS"> |
6c6cecf51bd0
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104 <param name="top_in" type="data" label="Input topology (top) file" format="top"/> |
6c6cecf51bd0
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105 <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/> |
6c6cecf51bd0
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106 </when> |
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107 </conditional> |
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108 <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand"> |
6c6cecf51bd0
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109 <sanitizer> |
6c6cecf51bd0
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110 <valid initial="string.printable"> |
6c6cecf51bd0
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111 <remove value="&"/> |
6c6cecf51bd0
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112 </valid> |
6c6cecf51bd0
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113 <mapping initial="none"> |
6c6cecf51bd0
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114 <add source="&" target="__and__"/> |
6c6cecf51bd0
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115 </mapping> |
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116 </sanitizer> |
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117 </param> |
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118 <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"> |
6c6cecf51bd0
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119 <sanitizer> |
6c6cecf51bd0
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120 <valid initial="string.printable"> |
6c6cecf51bd0
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121 <remove value="&"/> |
6c6cecf51bd0
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122 </valid> |
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123 <mapping initial="none"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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124 <add source="&" target="__and__"/> |
6c6cecf51bd0
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125 </mapping> |
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126 </sanitizer> |
6c6cecf51bd0
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127 </param> |
6c6cecf51bd0
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128 <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)"> |
6c6cecf51bd0
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129 <sanitizer> |
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130 <valid initial="string.printable"> |
6c6cecf51bd0
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131 <remove value="&"/> |
6c6cecf51bd0
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132 </valid> |
6c6cecf51bd0
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133 <mapping initial="none"> |
6c6cecf51bd0
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134 <add source="&" target="__and__"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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135 </mapping> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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136 </sanitizer> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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137 </param> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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138 <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)"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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139 <sanitizer> |
6c6cecf51bd0
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140 <valid initial="string.printable"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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141 <remove value="&"/> |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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142 </valid> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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143 <mapping initial="none"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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144 <add source="&" target="__and__"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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145 </mapping> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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146 </sanitizer> |
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147 </param> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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148 </inputs> |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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149 <outputs> |
6c6cecf51bd0
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150 <data format="txt" name="prmtop_ligand" label="ligand prmtop"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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151 <data format="txt" name="prmtop_receptor" label="receptor prmtop"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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152 <data format="txt" name="prmtop_complex" label="complex prmtop"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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153 <data format="txt" name="prmtop_solvatedcomplex" label="solvated complex prmtop"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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154 </outputs> |
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155 <tests> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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156 <test> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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157 <!--example in this test is not solvated but sufficient --> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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158 <param name="fmt" value="AMBER"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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159 <conditional name="param_inputs"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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160 <param name="top_in" value="complex.prmtop"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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161 </conditional> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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162 <param name="stripmask_ligand" value="!:RAL"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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163 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT,RAL"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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164 <param name="stripmask_complex" value=":NA,CL,SOL,WAT"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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165 <output name="prmtop_ligand"> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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166 <assert_contents> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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167 <has_text text=" 61 15"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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168 <has_text text="%FLAG MASS"/> |
6c6cecf51bd0
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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169 <has_text text="RAL"/> |
6c6cecf51bd0
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170 </assert_contents> |
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171 </output> |
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172 <output name="prmtop_receptor"> |
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173 <assert_contents> |
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174 <has_text text=" 3880 15"/> |
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175 <has_text text="%FLAG MASS"/> |
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176 <has_text text="ALA LEU"/> |
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177 <not_has_text text="RAL "/> |
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178 </assert_contents> |
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179 </output> |
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180 <output name="prmtop_complex"> |
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181 <assert_contents> |
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182 <has_text text=" 3941 15"/> |
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183 <has_text text="%FLAG MASS"/> |
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184 <has_text text="ALA LEU"/> |
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185 <has_text text="RAL"/> |
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186 </assert_contents> |
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187 </output> |
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188 </test> |
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189 <test> |
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190 <!--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! --> |
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191 <param name="fmt" value="GROMACS"/> |
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192 <conditional name="param_inputs"> |
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193 <param name="top_in" value="topol_solv.top"/> |
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194 <param name="str_in" value="solv_ions.gro"/> |
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195 </conditional> |
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196 <!-- pretending CL is a ligand --> |
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197 <param name="stripmask_ligand" value="!:CL"/> |
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198 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/> |
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199 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine --> |
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200 <param name="stripmask_solvatedcomplex" value=":1-500@O&!(:WAT|:LYS,ARG)"/> |
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201 <output name="prmtop_ligand"> |
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202 <assert_contents> |
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203 <has_text text=" 8 59"/> |
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204 <has_text text="%FLAG MASS"/> |
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205 <has_text text="CL"/> |
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206 </assert_contents> |
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207 </output> |
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208 <output name="prmtop_receptor"> |
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209 <assert_contents> |
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210 <has_text text=" 1960 59"/> |
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211 <has_text text="%FLAG MASS"/> |
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212 <has_text text="LYS VAL PHE "/> |
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213 <not_has_text text="CL "/> |
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214 </assert_contents> |
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215 </output> |
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216 <output name="prmtop_solvatedcomplex"> |
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217 <assert_contents> |
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218 <has_text text=" 38265 59"/> |
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219 <has_text text="%FLAG MASS"/> |
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220 <has_text text="LYS VAL PHE"/> |
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221 </assert_contents> |
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222 </output> |
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223 </test> |
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224 </tests> |
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225 <help> |
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226 <![CDATA[ |
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227 .. class:: infomark |
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228 |
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229 **What it does** |
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230 |
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231 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. |
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232 |
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233 .. class:: infomark |
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234 |
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235 **How it works** |
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236 |
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237 AmberTools ParmEd is used to strip unneeded atoms and save out the parameter files. The stripmasks are defined by the user. |
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238 |
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239 .. class:: infomark |
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240 |
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241 **Outputs created** |
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242 |
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243 prmtop files for the ligand, receptor, complex and solvated complex. |
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244 |
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245 .. class:: infomark |
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246 |
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247 **User guide and documentation** |
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248 |
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249 - The `AmberTools Manual`_ |
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250 - The `Parmed Documentation`_ |
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251 |
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252 |
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253 .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf |
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254 .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html |
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255 |
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256 |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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257 ]]> |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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258 </help> |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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259 <expand macro="citations"> |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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260 <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 |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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261 account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation> |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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262 </expand> |
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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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263 </tool> |