Mercurial > repos > galaxyp > openms_decoydatabase
comparison DecoyDatabase.xml @ 13:71a6c870aa48 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:22:51 +0000 |
| parents | 622bb8ee4942 |
| children | 25529df60a81 |
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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> |