Mercurial > repos > galaxyp > openms_psmfeatureextractor

comparison macros.xml @ 4:8d4b175e06b5 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:20:56 +0000
parents 54ff34feb43d
children 151e4b119c70
comparison
equal deleted inserted replaced
3:2bbe01546e77 4:8d4b175e06b5
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!
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 -->
2 <macros> 5 <macros>
6 <token name="@TOOL_VERSION@">2.5</token>
7 <token name="@GALAXY_VERSION@">0</token>
3 <xml name="requirements"> 8 <xml name="requirements">
4 <requirements> 9 <requirements>
5 <requirement type="package" version="2.3">openms</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
6 <requirement type="package" version="15.12.15.2">xtandem</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
7 <requirement type="package" version="1.0">fido</requirement> 12 <!-- makeblastdb for OMSSAAdapter -->
8 <requirement type="package" version="2017.07.21">msgf_plus</requirement> 13 <requirement type="package" version="2.9.0">blast</requirement>
14 <requirement type="package" version="8.0.192">openjdk</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>
9 <yield/> 19 <yield/>
10 </requirements> 20 </requirements>
11 </xml> 21 </xml>
12 <xml name="stdio"> 22 <xml name="stdio">
13 <stdio> 23 <stdio>
19 <xml name="references"> 29 <xml name="references">
20 <citations> 30 <citations>
21 <citation type="doi">doi:10.1186/1471-2105-9-163</citation> 31 <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
22 </citations> 32 </citations>
23 </xml> 33 </xml>
24 <xml name="advanced_options"> 34 <xml name="adv_opts_macro">
25 <conditional name="adv_opts"> 35 <conditional name="adv_opts_cond">
26 <param name="adv_opts_selector" type="select" label="Advanced Options"> 36 <param name="adv_opts_selector" type="select" label="Advanced Options">
27 <option value="basic" selected="True">Hide Advanced Options</option> 37 <option value="basic" selected="True">Hide Advanced Options</option>
28 <option value="advanced">Show Advanced Options</option> 38 <option value="advanced">Show Advanced Options</option>
29 </param> 39 </param>
30 <when value="basic"/> 40 <when value="basic"/>
31 <when value="advanced"> 41 <when value="advanced">
32 <yield/> 42 <yield/>
33 </when> 43 </when>
34 </conditional> 44 </conditional>
35 </xml> 45 </xml>
36 </macros> 46
47 <!-- sanitizers and validators -->
48 <xml name="list_string_val">
49 <validator type="regex" message="parameter must not start with $">^[^$]</validator>
50
51 <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
52 </xml>
53 <xml name="list_string_san">
54 <sanitizer>
55 <valid initial="string.printable">
56 <!-- <remove value="'"/>-->
57 <!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote -->
58 <!-- <remove value="`"/>-->
59 <!-- <remove value="$"/>-->
60 <!-- <remove value="&lt;"/>-->
61 <!--<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 & -->
62 <!--<remove value=";"/>-->
63 <!-- <remove value="#"/>-->
64 </valid>
65 </sanitizer>
66 </xml>
67 <xml name="list_float_valsan">
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]+)?)* *$</validator>
69 <yield/>
70 <sanitizer>
71 <valid initial="string.digits">
72 <add value=" "/>
73 <add value="."/>
74 <add value="E"/>
75 <add value="e"/>
76 <add value="+"/>
77 <add value="-"/>
78 </valid>
79 </sanitizer>
80 </xml>
81 <xml name="list_integer_valsan">
82 <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
83 <yield/>
84 <sanitizer>
85 <valid initial="string.digits">
86 <add value=" "/>
87 <add value="+"/>
88 <add value="-"/>
89 </valid>
90 </sanitizer>
91 </xml>
92
93 <!-- helper function to quote space separated strings -->
94 <token name="@QUOTE_FOO@">
95 #def quote(s):
96 #set $s = [ _ for _ in $s.split(" ") if _ != "" ]
97 #set $q = False
98 #for $i, $p in enumerate($s):
99 #if $p == "":
100 #continue
101 #end if
102 #if $p.startswith('"'):
103 #set $q = True
104 #end if
105 ## #if p.startswith('-'):
106 ## #set p = "\\" + p
107 ## #elif p.startswith('"-'):
108 ## #set p = "\\" + p[1:]
109 ## #end if
110 #if not $q:
111 #set $s[i] = '"%s"' % p
112 #end if
113 #if $p.endswith('"'):
114 #set $q = False
115 #end if
116 #end for
117 #return " ".join($s)
118 #end def
119 </token>
120
121 <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'}
123 #return m[o]
124 #end def
125 #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'}
127 #return m[g]
128 #end def
129 ]]></token></macros>