Mercurial > repos > galaxyp > openms_cruxadapter

comparison CruxAdapter.xml @ 2:aed7aeb6feec 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 20:05:24 +0000
parents a8dd6f1257ab
children a915cadc2f07
comparison
equal deleted inserted replaced
1:60b24c30af7d 2:aed7aeb6feec
69 <expand macro="list_string_san"/> 69 <expand macro="list_string_san"/>
70 </param> 70 </param>
71 <param name="run_percolator" argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/> 71 <param name="run_percolator" argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/>
72 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 72 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
73 <option value="custom-enzyme">custom-enzyme</option> 73 <option value="custom-enzyme">custom-enzyme</option>
74 <option value="arg-c">arg-c</option>
75 <option value="asp-n">asp-n</option>
76 <option value="iodosobenzoate">iodosobenzoate</option>
77 <option value="staph-protease">staph-protease</option>
78 <option value="proline-endopeptidase">proline-endopeptidase</option>
74 <option value="glu-c">glu-c</option> 79 <option value="glu-c">glu-c</option>
75 <option value="pepsin-a">pepsin-a</option> 80 <option value="pepsin-a">pepsin-a</option>
76 <option value="cyanogen-bromide">cyanogen-bromide</option> 81 <option value="cyanogen-bromide">cyanogen-bromide</option>
77 <option value="clostripain">clostripain</option> 82 <option value="clostripain">clostripain</option>
78 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 83 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
79 <option value="arg-c">arg-c</option>
80 <option value="asp-n">asp-n</option>
81 <option value="no-enzyme">no-enzyme</option> 84 <option value="no-enzyme">no-enzyme</option>
82 <option value="iodosobenzoate">iodosobenzoate</option> 85 <option value="chymotrypsin">chymotrypsin</option>
83 <option value="staph-protease">staph-protease</option> 86 <option value="trypsin/p">trypsin/p</option>
84 <option value="proline-endopeptidase">proline-endopeptidase</option>
85 <option value="elastase">elastase</option> 87 <option value="elastase">elastase</option>
86 <option value="chymotrypsin">chymotrypsin</option>
87 <option value="lys-c">lys-c</option> 88 <option value="lys-c">lys-c</option>
88 <option value="lys-n">lys-n</option> 89 <option value="lys-n">lys-n</option>
89 <option value="trypsin/p">trypsin/p</option>
90 <option value="trypsin" selected="true">trypsin</option> 90 <option value="trypsin" selected="true">trypsin</option>
91 <expand macro="list_string_san"/> 91 <expand macro="list_string_san"/>
92 </param> 92 </param>
93 <param name="digestion" argument="-digestion" display="radio" type="select" optional="false" label="Full, partial or non specific digestion" help=""> 93 <param name="digestion" argument="-digestion" display="radio" type="select" optional="false" label="Full, partial or non specific digestion" help="">
94 <option value="full-digest" selected="true">full-digest</option> 94 <option value="full-digest" selected="true">full-digest</option>
95 <option value="partial-digest">partial-digest</option> 95 <option value="partial-digest">partial-digest</option>
96 <option value="non-specific-digest">non-specific-digest</option> 96 <option value="non-specific-digest">non-specific-digest</option>
97 <expand macro="list_string_san"/> 97 <expand macro="list_string_san"/>
98 </param> 98 </param>
99 <param name="allowed_missed_cleavages" argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/> 99 <param name="allowed_missed_cleavages" argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/>
100 <param name="decoy_format" argument="-decoy-format" display="radio" type="select" optional="false" label="Decoy generation method either by reversing the sequence or shuffling it" help=""> 100 <param name="decoy_format" argument="-decoy_format" display="radio" type="select" optional="false" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
101 <option value="none">none</option> 101 <option value="none">none</option>
102 <option value="shuffle" selected="true">shuffle</option> 102 <option value="shuffle" selected="true">shuffle</option>
103 <option value="peptide-reverse">peptide-reverse</option> 103 <option value="peptide-reverse">peptide-reverse</option>
104 <option value="protein-reverse">protein-reverse</option> 104 <option value="protein-reverse">protein-reverse</option>
105 <expand macro="list_string_san"/> 105 <expand macro="list_string_san"/>
106 </param> 106 </param>
107 <param name="keep_terminal_aminos" argument="-keep-terminal-aminos" display="radio" type="select" optional="false" label="Whether to keep N and C terminal in place or also shuffled / reversed" help=""> 107 <param name="keep_terminal_aminos" argument="-keep_terminal_aminos" display="radio" type="select" optional="false" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
108 <option value="N">N</option> 108 <option value="N">N</option>
109 <option value="C">C</option> 109 <option value="C">C</option>
110 <option value="NC" selected="true">NC</option> 110 <option value="NC" selected="true">NC</option>
111 <option value="none">none</option> 111 <option value="none">none</option>
112 <expand macro="list_string_san"/> 112 <expand macro="list_string_san"/>
129 <param name="decoy_prefix" argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help=""> 129 <param name="decoy_prefix" argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help="">
130 <expand macro="list_string_san"/> 130 <expand macro="list_string_san"/>
131 </param> 131 </param>
132 <param name="deisotope" argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/> 132 <param name="deisotope" argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/>
133 <param name="report_decoys" argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/> 133 <param name="report_decoys" argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/>
134 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 134 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
135 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 135 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
136 <expand macro="list_string_san"/> 136 <expand macro="list_string_san"/>
137 </param> 137 </param>
138 </expand> 138 </expand>
139 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 139 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
140 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 140 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
141 </param> 141 </param>
142 </inputs> 142 </inputs>
143 <outputs> 143 <outputs>
144 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 144 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
151 <expand macro="manutest_CruxAdapter"/> 151 <expand macro="manutest_CruxAdapter"/>
152 </tests> 152 </tests>
153 <help><![CDATA[Identifies MS/MS spectra using Crux. 153 <help><![CDATA[Identifies MS/MS spectra using Crux.
154 154
155 155
156 For more information, visit http://www.openms.de/documentation/TOPP_CruxAdapter.html]]></help> 156 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CruxAdapter.html]]></help>
157 <expand macro="references"/> 157 <expand macro="references"/>
158 </tool> 158 </tool>