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comparison macros.xml @ 14:5c2a97a234d6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:15:43 +0000
parents 7f6a1f27553e
children 567de7cb1766
comparison
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13:7f6a1f27553e 14:5c2a97a234d6
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 &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
51 <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</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>