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annotate macros.xml @ 1:f9675543622a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:41:43 +0000
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fb0ebc6f97f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!-- CTD2Galaxy depends on this file and on the stdio, advanced_options macros!
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3 You can edit this file to add your own macros, if you so desire, or you can
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4 add additional macro files using the m/macros parameter -->
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5 <macros>
1
f9675543622a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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6 <token name="@TOOL_VERSION@">3.1</token>
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7 <token name="@VERSION_SUFFIX@">0</token>
1
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8 <token name="@TEST_DATA_LOCATION@"/>
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9 <xml name="requirements">
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
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12 <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
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13 <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter -->
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14 <requirement type="package" version="2.14.1">blast</requirement>
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15 <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
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16 <!-- for realpath (used e.g. in LuciphorAdapter) -->
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17 <!--<requirement type="package" version="8.25">coreutils</requirement>-->
1
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18 <requirement type="package" version="1.5">ctdopts</requirement>
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19 <yield/>
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20 </requirements>
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21 </xml>
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22 <xml name="stdio">
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23 <stdio>
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24 <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/>
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25 <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/>
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26 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
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27 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
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28 <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
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f9675543622a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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29 <regex match="OMSSA ran out of RAM" level="fatal_oom" description="Could not allocate memory"/>
f9675543622a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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30 <regex match="comet' crashed hard (segfault-like). Please check the log." level="fatal_oom" description="Could not allocate memory"/>
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31 </stdio>
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32 </xml>
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33 <xml name="references">
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34 <citations>
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35 <citation type="doi">doi:10.1186/1471-2105-9-163</citation>
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36 </citations>
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37 </xml>
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38 <xml name="adv_opts_macro">
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39 <section name="adv_opts" title="Advanced Options" expanded="false">
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40 <yield/>
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41 </section>
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42 </xml>
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43
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44 <!-- sanitizers and validators -->
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45 <xml name="list_string_val" token_name="">
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46 <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator>
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47 <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
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48 </xml>
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49 <xml name="list_string_san">
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50 <sanitizer>
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51 <valid initial="string.printable">
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52 <!-- <remove value="'"/>-->
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53 <!-- <remove value="\"/>--><!-- otherwise the user could quote the final quote -->
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54 <!-- <remove value="`"/>-->
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55 <!-- <remove value="$"/>-->
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56 <!-- <remove value="&lt;"/>-->
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57 <!--<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 & -->
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58 <!--<remove value=";"/>-->
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59 <!-- <remove value="#"/>-->
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60 </valid>
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61 </sanitizer>
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62 </xml>
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63 <xml name="list_float_valsan" token_name="">
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64 <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]+)?)* *$</validator>
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65 <yield/>
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66 <sanitizer>
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67 <valid initial="string.digits">
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68 <add value=" "/>
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69 <add value="."/>
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70 <add value="E"/>
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71 <add value="e"/>
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72 <add value="+"/>
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73 <add value="-"/>
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74 </valid>
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75 </sanitizer>
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76 </xml>
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77 <xml name="list_integer_valsan" token_name="">
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78 <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
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79 <yield/>
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80 <sanitizer>
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81 <valid initial="string.digits">
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82 <add value=" "/>
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83 <add value="+"/>
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84 <add value="-"/>
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85 </valid>
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86 </sanitizer>
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87 </xml>
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88
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89 <!-- helper function to quote space separated strings -->
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90 <token name="@QUOTE_FOO@">
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91 #def quote(s):
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92 #set $s = [ _ for _ in $s.split(" ") if _ != "" ]
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93 #set $q = False
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94 #for $i, $p in enumerate($s):
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95 #if $p == "":
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96 #continue
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97 #end if
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98 #if $p.startswith('"'):
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99 #set $q = True
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100 #end if
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101 ## #if p.startswith('-'):
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102 ## #set p = "\\" + p
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103 ## #elif p.startswith('"-'):
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104 ## #set p = "\\" + p[1:]
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105 ## #end if
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106 #if not $q:
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107 #set $s[i] = '"%s"' % p
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108 #end if
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109 #if $p.endswith('"'):
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110 #set $q = False
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111 #end if
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112 #end for
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113 #return " ".join($s)
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114 #end def
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115 </token>
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116
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117 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
1
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118 #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': 'xsd', 'zip': 'zip'}
0
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119 #return m[o]
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120 #end def
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121 #def gxy2omsext(g)
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122 #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', 'xsd': 'xsd', 'zip': 'zip'}
0
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123 #return m[g]
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124 #end def
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125 ]]></token></macros>