Mercurial > repos > galaxyp > openms_psmfeatureextractor

comparison macros.xml @ 10:63fea23042c4 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 19:01:06 +0000
parents 59736982ab7b
children c68cd6e1d3dc
comparison
equal deleted inserted replaced
9:047020d9012f 10:63fea23042c4
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/>
31 <citations> 32 <citations>
32 <citation type="doi">doi:10.1186/1471-2105-9-163</citation> 33 <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
33 </citations> 34 </citations>
34 </xml> 35 </xml>
35 <xml name="adv_opts_macro"> 36 <xml name="adv_opts_macro">
36 <conditional name="adv_opts_cond"> 37 <section name="adv_opts" title="Advanced Options" expanded="false">
37 <param name="adv_opts_selector" type="select" label="Advanced Options"> 38 <yield/>
38 <option value="basic" selected="True">Hide Advanced Options</option> 39 </section>
39 <option value="advanced">Show Advanced Options</option>
40 </param>
41 <when value="basic"/>
42 <when value="advanced">
43 <yield/>
44 </when>
45 </conditional>
46 </xml> 40 </xml>
47 41
48 <!-- sanitizers and validators --> 42 <!-- sanitizers and validators -->
49 <xml name="list_string_val"> 43 <xml name="list_string_val" token_name="">
50 <validator type="regex" message="parameter must not start with $">^[^$]</validator> 44 <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator>
51 45 <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
52 <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
53 </xml> 46 </xml>
54 <xml name="list_string_san"> 47 <xml name="list_string_san">
55 <sanitizer> 48 <sanitizer>
56 <valid initial="string.printable"> 49 <valid initial="string.printable">
57 <!-- <remove value="'"/>--> 50 <!-- <remove value="'"/>-->
63 <!--<remove value=";"/>--> 56 <!--<remove value=";"/>-->
64 <!-- <remove value="#"/>--> 57 <!-- <remove value="#"/>-->
65 </valid> 58 </valid>
66 </sanitizer> 59 </sanitizer>
67 </xml> 60 </xml>
68 <xml name="list_float_valsan"> 61 <xml name="list_float_valsan" token_name="">
69 <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>
70 <yield/> 63 <yield/>
71 <sanitizer> 64 <sanitizer>
72 <valid initial="string.digits"> 65 <valid initial="string.digits">
73 <add value=" "/> 66 <add value=" "/>
74 <add value="."/> 67 <add value="."/>
77 <add value="+"/> 70 <add value="+"/>
78 <add value="-"/> 71 <add value="-"/>
79 </valid> 72 </valid>
80 </sanitizer> 73 </sanitizer>
81 </xml> 74 </xml>
82 <xml name="list_integer_valsan"> 75 <xml name="list_integer_valsan" token_name="">
83 <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>
84 <yield/> 77 <yield/>
85 <sanitizer> 78 <sanitizer>
86 <valid initial="string.digits"> 79 <valid initial="string.digits">
87 <add value=" "/> 80 <add value=" "/>
88 <add value="+"/> 81 <add value="+"/>
118 #return " ".join($s) 111 #return " ".join($s)
119 #end def 112 #end def
120 </token> 113 </token>
121 114
122 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) 115 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
123 #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'}
124 #return m[o] 117 #return m[o]
125 #end def 118 #end def
126 #def gxy2omsext(g) 119 #def gxy2omsext(g)
127 #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'}
128 #return m[g] 121 #return m[g]
129 #end def 122 #end def
130 ]]></token></macros> 123 ]]></token></macros>