Mercurial > repos > galaxyp > openms_digestor
comparison Digestor.xml @ 12:4827e132ac53 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:19:57 +0000 |
| parents | 7af5860ae563 |
| children | 13399dc8f687 |
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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> |