Mercurial > repos > galaxyp > openms_demeanderize
view macros.xml @ 17:2425a98560f5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:01:59 +0000 |
parents | d2852a9e5550 |
children | 17547aceaf40 |
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<?xml version='1.0' encoding='UTF-8'?> <!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros! You can edit this file to add your own macros, if you so desire, or you can add additional macro files using the m/macros parameter --> <macros> <token name="@TOOL_VERSION@">2.8</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> <requirement type="package" version="2.1.9">omssa</requirement> <requirement type="package" version="2.13.0">blast</requirement> <!--<requirement type="package" version="5.0.0">tpp</requirement>--> <!-- for realpath (used e.g. in LuciphorAdapter) --> <!--<requirement type="package" version="8.25">coreutils</requirement>--> <requirement type="package" version="1.4">ctdopts</requirement> <yield/> </requirements> </xml> <xml name="stdio"> <stdio> <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/> <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/> <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> </stdio> </xml> <xml name="references"> <citations> <citation type="doi">doi:10.1186/1471-2105-9-163</citation> </citations> </xml> <xml name="adv_opts_macro"> <section name="adv_opts" title="Advanced Options" expanded="false"> <yield/> </section> </xml> <!-- sanitizers and validators --> <xml name="list_string_val" token_name=""> <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator> <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> </xml> <xml name="list_string_san"> <sanitizer> <valid initial="string.printable"> <!-- <remove value="'"/>--> <!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote --> <!-- <remove value="`"/>--> <!-- <remove value="$"/>--> <!-- <remove value="<"/>--> <!--<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 & --> <!--<remove value=";"/>--> <!-- <remove value="#"/>--> </valid> </sanitizer> </xml> <xml name="list_float_valsan" token_name=""> <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]+)?)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> <add value=" "/> <add value="."/> <add value="E"/> <add value="e"/> <add value="+"/> <add value="-"/> </valid> </sanitizer> </xml> <xml name="list_integer_valsan" token_name=""> <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> <add value=" "/> <add value="+"/> <add value="-"/> </valid> </sanitizer> </xml> <!-- helper function to quote space separated strings --> <token name="@QUOTE_FOO@"> #def quote(s): #set $s = [ _ for _ in $s.split(" ") if _ != "" ] #set $q = False #for $i, $p in enumerate($s): #if $p == "": #continue #end if #if $p.startswith('"'): #set $q = True #end if ## #if p.startswith('-'): ## #set p = "\\" + p ## #elif p.startswith('"-'): ## #set p = "\\" + p[1:] ## #end if #if not $q: #set $s[i] = '"%s"' % p #end if #if $p.endswith('"'): #set $q = False #end if #end for #return " ".join($s) #end def </token> <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) #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'} #return m[o] #end def #def gxy2omsext(g) #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'} #return m[g] #end def ]]></token></macros>