Mercurial > repos > galaxyp > openms_digestor

comparison Digestor.xml @ 12:4827e132ac53 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 20:19:57 +0000
parents 7af5860ae563
children 13399dc8f687
comparison
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11:ede260ee1404 12:4827e132ac53
49 </param> 49 </param>
50 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/> 50 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
51 <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/> 51 <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/>
52 <param name="max_length" argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/> 52 <param name="max_length" argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/>
53 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The type of digestion enzyme" help=""> 53 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The type of digestion enzyme" help="">
54 <option value="Asp-N">Asp-N</option> 54 <option value="V8-E">V8-E</option>
55 <option value="Asp-N/B">Asp-N/B</option> 55 <option value="leukocyte elastase">leukocyte elastase</option>
56 <option value="Asp-N_ambic">Asp-N_ambic</option> 56 <option value="proline endopeptidase">proline endopeptidase</option>
57 <option value="cyanogen-bromide">cyanogen-bromide</option> 57 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
58 <option value="Clostripain/P">Clostripain/P</option> 58 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
59 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 59 <option value="2-iodobenzoate">2-iodobenzoate</option>
60 <option value="no cleavage">no cleavage</option> 60 <option value="iodosobenzoate">iodosobenzoate</option>
61 <option value="unspecific cleavage">unspecific cleavage</option>
62 <option value="staphylococcal protease/D">staphylococcal protease/D</option> 61 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
63 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 62 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
64 <option value="Glu-C+P">Glu-C+P</option> 63 <option value="Glu-C+P">Glu-C+P</option>
65 <option value="PepsinA + P">PepsinA + P</option> 64 <option value="PepsinA + P">PepsinA + P</option>
66 <option value="leukocyte elastase">leukocyte elastase</option> 65 <option value="cyanogen-bromide">cyanogen-bromide</option>
67 <option value="proline endopeptidase">proline endopeptidase</option> 66 <option value="Clostripain/P">Clostripain/P</option>
67 <option value="Asp-N/B">Asp-N/B</option>
68 <option value="Asp-N_ambic">Asp-N_ambic</option>
68 <option value="Chymotrypsin">Chymotrypsin</option> 69 <option value="Chymotrypsin">Chymotrypsin</option>
69 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 70 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
70 <option value="CNBr">CNBr</option> 71 <option value="CNBr">CNBr</option>
71 <option value="Formic_acid">Formic_acid</option> 72 <option value="Formic_acid">Formic_acid</option>
72 <option value="Lys-C">Lys-C</option> 73 <option value="Lys-C">Lys-C</option>
73 <option value="Lys-N">Lys-N</option> 74 <option value="Lys-N">Lys-N</option>
74 <option value="Lys-C/P">Lys-C/P</option> 75 <option value="Lys-C/P">Lys-C/P</option>
76 <option value="Trypsin/P">Trypsin/P</option>
77 <option value="V8-DE">V8-DE</option>
78 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
79 <option value="no cleavage">no cleavage</option>
80 <option value="unspecific cleavage">unspecific cleavage</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>
75 <option value="PepsinA">PepsinA</option> 84 <option value="PepsinA">PepsinA</option>
76 <option value="TrypChymo">TrypChymo</option> 85 <option value="TrypChymo">TrypChymo</option>
77 <option value="Trypsin/P">Trypsin/P</option>
78 <option value="V8-DE">V8-DE</option>
79 <option value="V8-E">V8-E</option>
80 <option value="Arg-C">Arg-C</option>
81 <option value="Arg-C/P">Arg-C/P</option>
82 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
83 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
84 <option value="2-iodobenzoate">2-iodobenzoate</option>
85 <option value="iodosobenzoate">iodosobenzoate</option>
86 <option value="Trypsin" selected="true">Trypsin</option> 86 <option value="Trypsin" selected="true">Trypsin</option>
87 <expand macro="list_string_san"/> 87 <expand macro="list_string_san"/>
88 </param> 88 </param>
89 <section name="FASTA" title="Options for FASTA output files" help="" expanded="false"> 89 <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
90 <param name="ID" argument="-FASTA:ID" display="radio" type="select" optional="false" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help=""> 90 <param name="ID" argument="-FASTA:ID" display="radio" type="select" optional="false" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
98 <option value="keep">keep</option> 98 <option value="keep">keep</option>
99 <expand macro="list_string_san"/> 99 <expand macro="list_string_san"/>
100 </param> 100 </param>
101 </section> 101 </section>
102 <expand macro="adv_opts_macro"> 102 <expand macro="adv_opts_macro">
103 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 103 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
104 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 104 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
105 <expand macro="list_string_san"/> 105 <expand macro="list_string_san"/>
106 </param> 106 </param>
107 </expand> 107 </expand>
108 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 108 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
110 </param> 110 </param>
111 </inputs> 111 </inputs>
112 <outputs> 112 <outputs>
113 <data name="out" label="${tool.name} on ${on_string}: out"> 113 <data name="out" label="${tool.name} on ${on_string}: out">
125 <expand macro="manutest_Digestor"/> 125 <expand macro="manutest_Digestor"/>
126 </tests> 126 </tests>
127 <help><![CDATA[Digests a protein database in-silico. 127 <help><![CDATA[Digests a protein database in-silico.
128 128
129 129
130 For more information, visit http://www.openms.de/documentation/UTILS_Digestor.html]]></help> 130 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_Digestor.html]]></help>
131 <expand macro="references"/> 131 <expand macro="references"/>
132 </tool> 132 </tool>