Mercurial > repos > galaxyp > openms_demeanderize
comparison macros.xml @ 17:2425a98560f5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:01:59 +0000 |
parents | d2852a9e5550 |
children | 17547aceaf40 |
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16:d2852a9e5550 | 17:2425a98560f5 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros! | 2 <!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros! |
3 You can edit this file to add your own macros, if you so desire, or you can | 3 You can edit this file to add your own macros, if you so desire, or you can |
4 add additional macro files using the m/macros parameter --> | 4 add additional macro files using the m/macros parameter --> |
5 <macros> | 5 <macros> |
6 <token name="@TOOL_VERSION@">2.6</token> | 6 <token name="@TOOL_VERSION@">2.8</token> |
7 <token name="@GALAXY_VERSION@">0</token> | 7 <token name="@VERSION_SUFFIX@">0</token> |
8 <xml name="requirements"> | 8 <xml name="requirements"> |
9 <requirements> | 9 <requirements> |
10 <requirement type="package" version="@TOOL_VERSION@">openms</requirement> | 10 <requirement type="package" version="@TOOL_VERSION@">openms</requirement> |
11 <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> | 11 <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> |
12 <!-- makeblastdb for OMSSAAdapter --> | 12 <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> |
13 <requirement type="package" version="2.9.0">blast</requirement> | 13 <requirement type="package" version="2.1.9">omssa</requirement> |
14 <requirement type="package" version="2.13.0">blast</requirement> | |
14 <!--<requirement type="package" version="5.0.0">tpp</requirement>--> | 15 <!--<requirement type="package" version="5.0.0">tpp</requirement>--> |
15 <!-- for realpath (used e.g. in LuciphorAdapter) --> | 16 <!-- for realpath (used e.g. in LuciphorAdapter) --> |
16 <!--<requirement type="package" version="8.25">coreutils</requirement>--> | 17 <!--<requirement type="package" version="8.25">coreutils</requirement>--> |
17 <requirement type="package" version="1.4">ctdopts</requirement> | 18 <requirement type="package" version="1.4">ctdopts</requirement> |
18 <yield/> | 19 <yield/> |
19 </requirements> | 20 </requirements> |
20 </xml> | 21 </xml> |
21 <xml name="stdio"> | 22 <xml name="stdio"> |
22 <stdio> | 23 <stdio> |
23 <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/> | 24 <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/> |
25 <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/> | |
24 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> | 26 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> |
25 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> | 27 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> |
26 <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> | 28 <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> |
27 </stdio> | 29 </stdio> |
28 </xml> | 30 </xml> |
30 <citations> | 32 <citations> |
31 <citation type="doi">doi:10.1186/1471-2105-9-163</citation> | 33 <citation type="doi">doi:10.1186/1471-2105-9-163</citation> |
32 </citations> | 34 </citations> |
33 </xml> | 35 </xml> |
34 <xml name="adv_opts_macro"> | 36 <xml name="adv_opts_macro"> |
35 <conditional name="adv_opts_cond"> | 37 <section name="adv_opts" title="Advanced Options" expanded="false"> |
36 <param name="adv_opts_selector" type="select" label="Advanced Options"> | 38 <yield/> |
37 <option value="basic" selected="True">Hide Advanced Options</option> | 39 </section> |
38 <option value="advanced">Show Advanced Options</option> | |
39 </param> | |
40 <when value="basic"/> | |
41 <when value="advanced"> | |
42 <yield/> | |
43 </when> | |
44 </conditional> | |
45 </xml> | 40 </xml> |
46 | 41 |
47 <!-- sanitizers and validators --> | 42 <!-- sanitizers and validators --> |
48 <xml name="list_string_val"> | 43 <xml name="list_string_val" token_name=""> |
49 <validator type="regex" message="parameter must not start with $">^[^$]</validator> | 44 <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator> |
50 | 45 <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> |
51 <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> | |
52 </xml> | 46 </xml> |
53 <xml name="list_string_san"> | 47 <xml name="list_string_san"> |
54 <sanitizer> | 48 <sanitizer> |
55 <valid initial="string.printable"> | 49 <valid initial="string.printable"> |
56 <!-- <remove value="'"/>--> | 50 <!-- <remove value="'"/>--> |
62 <!--<remove value=";"/>--> | 56 <!--<remove value=";"/>--> |
63 <!-- <remove value="#"/>--> | 57 <!-- <remove value="#"/>--> |
64 </valid> | 58 </valid> |
65 </sanitizer> | 59 </sanitizer> |
66 </xml> | 60 </xml> |
67 <xml name="list_float_valsan"> | 61 <xml name="list_float_valsan" token_name=""> |
68 <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> | 62 <validator type="regex" message="parameter @NAME@: a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> |
69 <yield/> | 63 <yield/> |
70 <sanitizer> | 64 <sanitizer> |
71 <valid initial="string.digits"> | 65 <valid initial="string.digits"> |
72 <add value=" "/> | 66 <add value=" "/> |
73 <add value="."/> | 67 <add value="."/> |
76 <add value="+"/> | 70 <add value="+"/> |
77 <add value="-"/> | 71 <add value="-"/> |
78 </valid> | 72 </valid> |
79 </sanitizer> | 73 </sanitizer> |
80 </xml> | 74 </xml> |
81 <xml name="list_integer_valsan"> | 75 <xml name="list_integer_valsan" token_name=""> |
82 <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> | 76 <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> |
83 <yield/> | 77 <yield/> |
84 <sanitizer> | 78 <sanitizer> |
85 <valid initial="string.digits"> | 79 <valid initial="string.digits"> |
86 <add value=" "/> | 80 <add value=" "/> |
87 <add value="+"/> | 81 <add value="+"/> |
117 #return " ".join($s) | 111 #return " ".join($s) |
118 #end def | 112 #end def |
119 </token> | 113 </token> |
120 | 114 |
121 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) | 115 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) |
122 #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} | 116 #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} |
123 #return m[o] | 117 #return m[o] |
124 #end def | 118 #end def |
125 #def gxy2omsext(g) | 119 #def gxy2omsext(g) |
126 #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} | 120 #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} |
127 #return m[g] | 121 #return m[g] |
128 #end def | 122 #end def |
129 ]]></token></macros> | 123 ]]></token></macros> |