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comparison DigestorMotif.xml @ 13:3138bbc00588 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:43:43 +0000
parents 01f5e95b5961
children
comparison
equal deleted inserted replaced
12:01f5e95b5961 13:3138bbc00588
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 CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>digests a protein database in-silico</description> 4 <description>digests a protein database in-silico</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">DigestorMotif</token> 6 <token name="@EXECUTABLE@">DigestorMotif</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/> 41 <param argument="-in" type="data" format="fasta" label="FASTA input file" help=" select fasta data sets(s)"/>
43 <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/> 42 <param argument="-missed_cleavages" type="integer" min="0" value="1" label="the number of allowed missed cleavages" help=""/>
44 <param argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/> 43 <param argument="-mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help=""/>
45 <param argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/> 44 <param argument="-min_length" type="integer" value="6" label="minimum length of peptide" help=""/>
46 <param argument="-out_option" type="integer" optional="true" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/> 45 <param argument="-out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/>
47 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> 46 <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
48 <option value="Arg-C/P">Arg-C/P</option> 47 <option value="Trypsin/P">Trypsin/P</option>
49 <option value="Asp-N">Asp-N</option> 48 <option value="V8-DE">V8-DE</option>
50 <option value="Asp-N/B">Asp-N/B</option> 49 <option value="V8-E">V8-E</option>
51 <option value="Arg-C">Arg-C</option> 50 <option value="leukocyte elastase">leukocyte elastase</option>
51 <option value="proline endopeptidase">proline endopeptidase</option>
52 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 52 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
53 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 53 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
54 <option value="no cleavage">no cleavage</option> 54 <option value="2-iodobenzoate">2-iodobenzoate</option>
55 <option value="unspecific cleavage">unspecific cleavage</option> 55 <option value="iodosobenzoate">iodosobenzoate</option>
56 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
57 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
56 <option value="Glu-C+P">Glu-C+P</option> 58 <option value="Glu-C+P">Glu-C+P</option>
57 <option value="PepsinA + P">PepsinA + P</option> 59 <option value="PepsinA + P">PepsinA + P</option>
58 <option value="cyanogen-bromide">cyanogen-bromide</option> 60 <option value="cyanogen-bromide">cyanogen-bromide</option>
59 <option value="Clostripain/P">Clostripain/P</option> 61 <option value="Clostripain/P">Clostripain/P</option>
60 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 62 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
63 <option value="no cleavage">no cleavage</option>
64 <option value="unspecific cleavage">unspecific cleavage</option>
61 <option value="Asp-N_ambic">Asp-N_ambic</option> 65 <option value="Asp-N_ambic">Asp-N_ambic</option>
62 <option value="Chymotrypsin">Chymotrypsin</option> 66 <option value="Chymotrypsin">Chymotrypsin</option>
63 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 67 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
64 <option value="CNBr">CNBr</option> 68 <option value="CNBr">CNBr</option>
65 <option value="Formic_acid">Formic_acid</option> 69 <option value="Formic_acid">Formic_acid</option>
66 <option value="Lys-C">Lys-C</option> 70 <option value="Lys-C">Lys-C</option>
71 <option value="Trypsin" selected="true">Trypsin</option>
72 <option value="Arg-C">Arg-C</option>
73 <option value="Arg-C/P">Arg-C/P</option>
74 <option value="Asp-N">Asp-N</option>
75 <option value="Asp-N/B">Asp-N/B</option>
67 <option value="Lys-N">Lys-N</option> 76 <option value="Lys-N">Lys-N</option>
68 <option value="Lys-C/P">Lys-C/P</option> 77 <option value="Lys-C/P">Lys-C/P</option>
69 <option value="PepsinA">PepsinA</option> 78 <option value="PepsinA">PepsinA</option>
70 <option value="TrypChymo">TrypChymo</option> 79 <option value="TrypChymo">TrypChymo</option>
71 <option value="Trypsin/P">Trypsin/P</option>
72 <option value="V8-DE">V8-DE</option>
73 <option value="V8-E">V8-E</option>
74 <option value="leukocyte elastase">leukocyte elastase</option>
75 <option value="proline endopeptidase">proline endopeptidase</option>
76 <option value="2-iodobenzoate">2-iodobenzoate</option>
77 <option value="iodosobenzoate">iodosobenzoate</option>
78 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
79 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
80 <option value="Trypsin" selected="true">Trypsin</option>
81 <expand macro="list_string_san" name="enzyme"/> 80 <expand macro="list_string_san" name="enzyme"/>
82 </param> 81 </param>
83 <param argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help=""> 82 <param argument="-motif" type="text" value="M" label="the motif for the restricted peptidome" help="">
84 <expand macro="list_string_san" name="motif"/> 83 <expand macro="list_string_san" name="motif"/>
85 </param> 84 </param>
86 <expand macro="adv_opts_macro"> 85 <expand macro="adv_opts_macro">
87 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 86 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
88 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 87 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
89 <expand macro="list_string_san" name="test"/> 88 <expand macro="list_string_san" name="test"/>
90 </param> 89 </param>
91 </expand> 90 </expand>
92 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
101 </outputs> 100 </outputs>
102 <tests/> 101 <tests/>
103 <help><![CDATA[digests a protein database in-silico 102 <help><![CDATA[digests a protein database in-silico
104 103
105 104
106 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DigestorMotif.html]]></help> 105 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DigestorMotif.html]]></help>
107 <expand macro="references"/> 106 <expand macro="references"/>
108 </tool> 107 </tool>