Mercurial > repos > galaxyp > openms_decoydatabase

comparison DecoyDatabase.xml @ 13:71a6c870aa48 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 20:22:51 +0000
parents 622bb8ee4942
children 25529df60a81
comparison
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12:24fd374cbffc 13:71a6c870aa48
60 <option value="reverse" selected="true">reverse</option> 60 <option value="reverse" selected="true">reverse</option>
61 <option value="shuffle">shuffle</option> 61 <option value="shuffle">shuffle</option>
62 <expand macro="list_string_san"/> 62 <expand macro="list_string_san"/>
63 </param> 63 </param>
64 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="Enzyme used for the digestion of the sample" help="Only applicable if parameter 'type' is 'protein'"> 64 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="Enzyme used for the digestion of the sample" help="Only applicable if parameter 'type' is 'protein'">
65 <option value="Asp-N">Asp-N</option> 65 <option value="unspecific cleavage">unspecific cleavage</option>
66 <option value="Asp-N/B">Asp-N/B</option>
67 <option value="Asp-N_ambic">Asp-N_ambic</option>
68 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 66 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
69 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 67 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
70 <option value="Glu-C+P">Glu-C+P</option> 68 <option value="2-iodobenzoate">2-iodobenzoate</option>
71 <option value="PepsinA + P">PepsinA + P</option> 69 <option value="iodosobenzoate">iodosobenzoate</option>
72 <option value="cyanogen-bromide">cyanogen-bromide</option> 70 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
73 <option value="Clostripain/P">Clostripain/P</option>
74 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
75 <option value="Chymotrypsin">Chymotrypsin</option> 71 <option value="Chymotrypsin">Chymotrypsin</option>
76 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 72 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
77 <option value="CNBr">CNBr</option> 73 <option value="CNBr">CNBr</option>
78 <option value="Formic_acid">Formic_acid</option> 74 <option value="Formic_acid">Formic_acid</option>
79 <option value="Lys-C">Lys-C</option> 75 <option value="Lys-C">Lys-C</option>
80 <option value="Lys-N">Lys-N</option> 76 <option value="Lys-N">Lys-N</option>
81 <option value="Lys-C/P">Lys-C/P</option> 77 <option value="Lys-C/P">Lys-C/P</option>
82 <option value="PepsinA">PepsinA</option> 78 <option value="PepsinA">PepsinA</option>
83 <option value="TrypChymo">TrypChymo</option> 79 <option value="TrypChymo">TrypChymo</option>
84 <option value="Trypsin/P">Trypsin/P</option> 80 <option value="Trypsin/P">Trypsin/P</option>
81 <option value="Arg-C">Arg-C</option>
82 <option value="Arg-C/P">Arg-C/P</option>
83 <option value="Asp-N">Asp-N</option>
84 <option value="Asp-N/B">Asp-N/B</option>
85 <option value="Asp-N_ambic">Asp-N_ambic</option>
86 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
87 <option value="Glu-C+P">Glu-C+P</option>
88 <option value="PepsinA + P">PepsinA + P</option>
89 <option value="cyanogen-bromide">cyanogen-bromide</option>
90 <option value="Clostripain/P">Clostripain/P</option>
91 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
92 <option value="no cleavage">no cleavage</option>
85 <option value="V8-DE">V8-DE</option> 93 <option value="V8-DE">V8-DE</option>
86 <option value="V8-E">V8-E</option> 94 <option value="V8-E">V8-E</option>
87 <option value="leukocyte elastase">leukocyte elastase</option> 95 <option value="leukocyte elastase">leukocyte elastase</option>
88 <option value="proline endopeptidase">proline endopeptidase</option> 96 <option value="proline endopeptidase">proline endopeptidase</option>
89 <option value="no cleavage">no cleavage</option>
90 <option value="unspecific cleavage">unspecific cleavage</option>
91 <option value="Arg-C">Arg-C</option>
92 <option value="Arg-C/P">Arg-C/P</option>
93 <option value="2-iodobenzoate">2-iodobenzoate</option>
94 <option value="iodosobenzoate">iodosobenzoate</option>
95 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
96 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
97 <option value="Trypsin" selected="true">Trypsin</option> 97 <option value="Trypsin" selected="true">Trypsin</option>
98 <expand macro="list_string_san"/> 98 <expand macro="list_string_san"/>
99 </param> 99 </param>
100 <section name="Decoy" title="Decoy parameters section" help="" expanded="false"> 100 <section name="Decoy" title="Decoy parameters section" help="" expanded="false">
101 <param name="non_shuffle_pattern" argument="-Decoy:non_shuffle_pattern" type="text" optional="true" value="" label="Residues to not shuffle (keep at a constant position when shuffling)" help="Separate by comma, e.g. use 'K,P,R' here"> 101 <param name="non_shuffle_pattern" argument="-Decoy:non_shuffle_pattern" type="text" optional="true" value="" label="Residues to not shuffle (keep at a constant position when shuffling)" help="Separate by comma, e.g. use 'K,P,R' here">
108 <param name="shuffle_max_attempts" argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/> 108 <param name="shuffle_max_attempts" argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
109 <param name="shuffle_sequence_identity_threshold" argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help="If the sequence identity is above this threshold, shuffling is repeated. In case of repeated failure, individual amino acids are 'mutated' to produce a different amino acid sequence"/> 109 <param name="shuffle_sequence_identity_threshold" argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help="If the sequence identity is above this threshold, shuffling is repeated. In case of repeated failure, individual amino acids are 'mutated' to produce a different amino acid sequence"/>
110 <param name="seed" argument="-seed" type="text" optional="true" value="1" label="Random number seed (use 'time' for system time)" help=""> 110 <param name="seed" argument="-seed" type="text" optional="true" value="1" label="Random number seed (use 'time' for system time)" help="">
111 <expand macro="list_string_san"/> 111 <expand macro="list_string_san"/>
112 </param> 112 </param>
113 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 113 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
114 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 114 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
115 <expand macro="list_string_san"/> 115 <expand macro="list_string_san"/>
116 </param> 116 </param>
117 </expand> 117 </expand>
118 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 118 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
119 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 119 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
120 </param> 120 </param>
121 </inputs> 121 </inputs>
122 <outputs> 122 <outputs>
123 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/> 123 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
130 <expand macro="manutest_DecoyDatabase"/> 130 <expand macro="manutest_DecoyDatabase"/>
131 </tests> 131 </tests>
132 <help><![CDATA[Create decoy sequence database from forward sequence database. 132 <help><![CDATA[Create decoy sequence database from forward sequence database.
133 133
134 134
135 For more information, visit http://www.openms.de/documentation/UTILS_DecoyDatabase.html]]></help> 135 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DecoyDatabase.html]]></help>
136 <expand macro="references"/> 136 <expand macro="references"/>
137 </tool> 137 </tool>