Mercurial > repos > galaxyp > openms_digestor
comparison Digestor.xml @ 0:e661b6359f66 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:34:47 -0500 |
| parents | |
| children | 62341892592a |
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| -1:000000000000 | 0:e661b6359f66 |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
| 3 <!--Proposed Tool Section: [Utilities]--> | |
| 4 <tool id="Digestor" name="Digestor" version="2.1.0"> | |
| 5 <description>Digests a protein database in-silico.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">Digestor</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>Digestor | |
| 14 | |
| 15 #if $param_in: | |
| 16 -in $param_in | |
| 17 #end if | |
| 18 #if $param_out: | |
| 19 -out $param_out | |
| 20 #end if | |
| 21 #if $param_out_type: | |
| 22 -out_type | |
| 23 #if " " in str($param_out_type): | |
| 24 "$param_out_type" | |
| 25 #else | |
| 26 $param_out_type | |
| 27 #end if | |
| 28 #end if | |
| 29 #if $param_missed_cleavages: | |
| 30 -missed_cleavages $param_missed_cleavages | |
| 31 #end if | |
| 32 #if $param_min_length: | |
| 33 -min_length $param_min_length | |
| 34 #end if | |
| 35 #if $param_max_length: | |
| 36 -max_length $param_max_length | |
| 37 #end if | |
| 38 #if $param_enzyme: | |
| 39 -enzyme $param_enzyme | |
| 40 #end if | |
| 41 #if $adv_opts.adv_opts_selector=='advanced': | |
| 42 #if $adv_opts.param_force: | |
| 43 -force | |
| 44 #end if | |
| 45 #end if | |
| 46 </command> | |
| 47 <inputs> | |
| 48 <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in) "/> | |
| 49 <param name="param_out_type" display="radio" type="select" optional="True" label="Set this if you cannot control the filename of 'out'," help="(-out_type) e.g., in TOPPAS"> | |
| 50 <option value="idXML">idXML</option> | |
| 51 <option value="fasta">fasta</option> | |
| 52 </param> | |
| 53 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages) "/> | |
| 54 <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length) "/> | |
| 55 <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length) "/> | |
| 56 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme) "> | |
| 57 <option value="V8-E">V8-E</option> | |
| 58 <option value="TrypChymo">TrypChymo</option> | |
| 59 <option value="no cleavage">no cleavage</option> | |
| 60 <option value="Lys-C/P">Lys-C/P</option> | |
| 61 <option value="Asp-N">Asp-N</option> | |
| 62 <option value="Asp-N_ambic">Asp-N_ambic</option> | |
| 63 <option value="V8-DE">V8-DE</option> | |
| 64 <option value="Lys-C">Lys-C</option> | |
| 65 <option value="Trypsin" selected="true">Trypsin</option> | |
| 66 <option value="unspecific cleavage">unspecific cleavage</option> | |
| 67 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> | |
| 68 <option value="2-iodobenzoate">2-iodobenzoate</option> | |
| 69 <option value="leukocyte elastase">leukocyte elastase</option> | |
| 70 <option value="proline endopeptidase">proline endopeptidase</option> | |
| 71 <option value="CNBr">CNBr</option> | |
| 72 <option value="PepsinA">PepsinA</option> | |
| 73 <option value="Trypsin/P">Trypsin/P</option> | |
| 74 <option value="Arg-C">Arg-C</option> | |
| 75 <option value="Formic_acid">Formic_acid</option> | |
| 76 <option value="Chymotrypsin">Chymotrypsin</option> | |
| 77 </param> | |
| 78 <expand macro="advanced_options"> | |
| 79 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 80 </expand> | |
| 81 </inputs> | |
| 82 <outputs> | |
| 83 <data name="param_out" format="fasta"/> | |
| 84 </outputs> | |
| 85 <help>Digests a protein database in-silico. | |
| 86 | |
| 87 | |
| 88 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help> | |
| 89 </tool> |