Mercurial > repos > galaxyp > openms_cruxadapter
comparison CruxAdapter.xml @ 2:aed7aeb6feec draft
"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> |