Mercurial > repos > galaxyp > openms_openmsdatabasesinfo

comparison macros.xml @ 0:a7ff1eeba91f 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 19:23:33 +0000
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children ea9291282c0f
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-1:000000000000 0:a7ff1eeba91f
1 <?xml version='1.0' encoding='UTF-8'?>
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
4 add additional macro files using the m/macros parameter -->
5 <macros>
6 <token name="@TOOL_VERSION@">2.8</token>
7 <token name="@VERSION_SUFFIX@">0</token>
8 <xml name="requirements">
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
11 <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
12 <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter -->
13 <requirement type="package" version="2.1.9">omssa</requirement>
14 <requirement type="package" version="2.13.0">blast</requirement>
15 <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
16 <!-- for realpath (used e.g. in LuciphorAdapter) -->
17 <!--<requirement type="package" version="8.25">coreutils</requirement>-->
18 <requirement type="package" version="1.4">ctdopts</requirement>
19 <yield/>
20 </requirements>
21 </xml>
22 <xml name="stdio">
23 <stdio>
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"/>
26 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
27 <regex match="Cannot create VM thread" 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"/>
29 </stdio>
30 </xml>
31 <xml name="references">
32 <citations>
33 <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
34 </citations>
35 </xml>
36 <xml name="adv_opts_macro">
37 <section name="adv_opts" title="Advanced Options" expanded="false">
38 <yield/>
39 </section>
40 </xml>
41
42 <!-- sanitizers and validators -->
43 <xml name="list_string_val" token_name="">
44 <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator>
45 <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
46 </xml>
47 <xml name="list_string_san">
48 <sanitizer>
49 <valid initial="string.printable">
50 <!-- <remove value="'"/>-->
51 <!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote -->
52 <!-- <remove value="`"/>-->
53 <!-- <remove value="$"/>-->
54 <!-- <remove value="&lt;"/>-->
55 <!--<remove value="&amp;"/> removed for MascotAdapterOnline -Mascot_server:export_params which is a URL POST string which can contain & .. could be mapped to &amp; but there is still a & -->
56 <!--<remove value=";"/>-->
57 <!-- <remove value="#"/>-->
58 </valid>
59 </sanitizer>
60 </xml>
61 <xml name="list_float_valsan" token_name="">
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]+)?)* *$</validator>
63 <yield/>
64 <sanitizer>
65 <valid initial="string.digits">
66 <add value=" "/>
67 <add value="."/>
68 <add value="E"/>
69 <add value="e"/>
70 <add value="+"/>
71 <add value="-"/>
72 </valid>
73 </sanitizer>
74 </xml>
75 <xml name="list_integer_valsan" token_name="">
76 <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
77 <yield/>
78 <sanitizer>
79 <valid initial="string.digits">
80 <add value=" "/>
81 <add value="+"/>
82 <add value="-"/>
83 </valid>
84 </sanitizer>
85 </xml>
86
87 <!-- helper function to quote space separated strings -->
88 <token name="@QUOTE_FOO@">
89 #def quote(s):
90 #set $s = [ _ for _ in $s.split(" ") if _ != "" ]
91 #set $q = False
92 #for $i, $p in enumerate($s):
93 #if $p == "":
94 #continue
95 #end if
96 #if $p.startswith('"'):
97 #set $q = True
98 #end if
99 ## #if p.startswith('-'):
100 ## #set p = "\\" + p
101 ## #elif p.startswith('"-'):
102 ## #set p = "\\" + p[1:]
103 ## #end if
104 #if not $q:
105 #set $s[i] = '"%s"' % p
106 #end if
107 #if $p.endswith('"'):
108 #set $q = False
109 #end if
110 #end for
111 #return " ".join($s)
112 #end def
113 </token>
114
115 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
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'}
117 #return m[o]
118 #end def
119 #def gxy2omsext(g)
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'}
121 #return m[g]
122 #end def
123 ]]></token></macros>