Mercurial > repos > galaxyp > openms_textexporter
comparison macros.xml @ 9:27aeff17fd2e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 27 Aug 2020 19:45:29 -0400 |
parents | 3a2a31d4032c |
children | 1c596fdaf34a |
comparison
equal
deleted
inserted
replaced
8:1294873c8d1d | 9:27aeff17fd2e |
---|---|
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 ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> | |
52 </xml> | |
53 <xml name="list_string_san"> | |
54 <sanitizer> | |
55 <valid initial="string.printable"> | |
56 <!-- <remove value="'"/>--> | |
57 <!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote --> | |
58 <!-- <remove value="`"/>--> | |
59 <!-- <remove value="$"/>--> | |
60 <!-- <remove value="<"/>--> | |
61 <!--<remove value="&"/> removed for MascotAdapterOnline -Mascot_server:export_params which is a URL POST string which can contain & .. could be mapped to & 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> |