Mercurial > repos > galaxyp > openms_databasesuitability

comparison macros.xml @ 0:d994c72a91fc draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:54:23 +0000
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children 594a165c069c
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-1:000000000000 0:d994c72a91fc
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@">2.6</token>
7 <token name="@GALAXY_VERSION@">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 <!-- makeblastdb for OMSSAAdapter -->
13 <requirement type="package" version="2.9.0">blast</requirement>
14 <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
15 <!-- for realpath (used e.g. in LuciphorAdapter) -->
16 <!--<requirement type="package" version="8.25">coreutils</requirement>-->
17 <requirement type="package" version="1.4">ctdopts</requirement>
18 <yield/>
19 </requirements>
20 </xml>
21 <xml name="stdio">
22 <stdio>
23 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
24 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
25 <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
26 </stdio>
27 </xml>
28 <xml name="references">
29 <citations>
30 <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
31 </citations>
32 </xml>
33 <xml name="adv_opts_macro">
34 <conditional name="adv_opts_cond">
35 <param name="adv_opts_selector" type="select" label="Advanced Options">
36 <option value="basic" selected="True">Hide Advanced Options</option>
37 <option value="advanced">Show Advanced Options</option>
38 </param>
39 <when value="basic"/>
40 <when value="advanced">
41 <yield/>
42 </when>
43 </conditional>
44 </xml>
45
46 <!-- sanitizers and validators -->
47 <xml name="list_string_val">
48 <validator type="regex" message="parameter must not start with $">^[^$]</validator>
49
50 <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
51 </xml>
52 <xml name="list_string_san">
53 <sanitizer>
54 <valid initial="string.printable">
55 <!-- <remove value="'"/>-->
56 <!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote -->
57 <!-- <remove value="`"/>-->
58 <!-- <remove value="$"/>-->
59 <!-- <remove value="&lt;"/>-->
60 <!--<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 & -->
61 <!--<remove value=";"/>-->
62 <!-- <remove value="#"/>-->
63 </valid>
64 </sanitizer>
65 </xml>
66 <xml name="list_float_valsan">
67 <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]+)?)* *$</validator>
68 <yield/>
69 <sanitizer>
70 <valid initial="string.digits">
71 <add value=" "/>
72 <add value="."/>
73 <add value="E"/>
74 <add value="e"/>
75 <add value="+"/>
76 <add value="-"/>
77 </valid>
78 </sanitizer>
79 </xml>
80 <xml name="list_integer_valsan">
81 <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
82 <yield/>
83 <sanitizer>
84 <valid initial="string.digits">
85 <add value=" "/>
86 <add value="+"/>
87 <add value="-"/>
88 </valid>
89 </sanitizer>
90 </xml>
91
92 <!-- helper function to quote space separated strings -->
93 <token name="@QUOTE_FOO@">
94 #def quote(s):
95 #set $s = [ _ for _ in $s.split(" ") if _ != "" ]
96 #set $q = False
97 #for $i, $p in enumerate($s):
98 #if $p == "":
99 #continue
100 #end if
101 #if $p.startswith('"'):
102 #set $q = True
103 #end if
104 ## #if p.startswith('-'):
105 ## #set p = "\\" + p
106 ## #elif p.startswith('"-'):
107 ## #set p = "\\" + p[1:]
108 ## #end if
109 #if not $q:
110 #set $s[i] = '"%s"' % p
111 #end if
112 #if $p.endswith('"'):
113 #set $q = False
114 #end if
115 #end for
116 #return " ".join($s)
117 #end def
118 </token>
119
120 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
121 #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'}
122 #return m[o]
123 #end def
124 #def gxy2omsext(g)
125 #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'}
126 #return m[g]
127 #end def
128 ]]></token></macros>