Mercurial > repos > galaxyp > openms_digestormotif
comparison DigestorMotif.xml @ 12:01f5e95b5961 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:22:51 +0000 |
parents | bc7bd4710c4e |
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11:38676a2713f5 | 12:01f5e95b5961 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 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.--> | 2 <!--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]--> | 3 <!--Proposed Tool Section: [Utilities]--> |
4 <tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>digests a protein database in-silico</description> | 5 <description>digests a protein database in-silico</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">DigestorMotif</token> | 7 <token name="@EXECUTABLE@">DigestorMotif</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
39 <configfiles> | 37 <configfiles> |
40 <inputs name="args_json" data_style="paths"/> | 38 <inputs name="args_json" data_style="paths"/> |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | 40 </configfiles> |
43 <inputs> | 41 <inputs> |
44 <param name="in" argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/> | 42 <param argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/> |
45 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/> | 43 <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/> |
46 <param name="mass_accuracy" argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/> | 44 <param argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/> |
47 <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/> | 45 <param argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/> |
48 <param name="out_option" argument="-out_option" type="integer" optional="true" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" 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=""/> |
49 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> | 47 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> |
48 <option value="Arg-C/P">Arg-C/P</option> | |
49 <option value="Asp-N">Asp-N</option> | |
50 <option value="Asp-N/B">Asp-N/B</option> | |
51 <option value="Arg-C">Arg-C</option> | |
52 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> | |
50 <option value="Alpha-lytic protease">Alpha-lytic protease</option> | 53 <option value="Alpha-lytic protease">Alpha-lytic protease</option> |
51 <option value="2-iodobenzoate">2-iodobenzoate</option> | 54 <option value="no cleavage">no cleavage</option> |
52 <option value="iodosobenzoate">iodosobenzoate</option> | 55 <option value="unspecific cleavage">unspecific cleavage</option> |
53 <option value="staphylococcal protease/D">staphylococcal protease/D</option> | |
54 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> | |
55 <option value="Glu-C+P">Glu-C+P</option> | 56 <option value="Glu-C+P">Glu-C+P</option> |
56 <option value="PepsinA + P">PepsinA + P</option> | 57 <option value="PepsinA + P">PepsinA + P</option> |
57 <option value="cyanogen-bromide">cyanogen-bromide</option> | 58 <option value="cyanogen-bromide">cyanogen-bromide</option> |
58 <option value="Clostripain/P">Clostripain/P</option> | 59 <option value="Clostripain/P">Clostripain/P</option> |
59 <option value="Asp-N/B">Asp-N/B</option> | 60 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> |
60 <option value="Asp-N_ambic">Asp-N_ambic</option> | 61 <option value="Asp-N_ambic">Asp-N_ambic</option> |
61 <option value="Chymotrypsin">Chymotrypsin</option> | 62 <option value="Chymotrypsin">Chymotrypsin</option> |
62 <option value="Chymotrypsin/P">Chymotrypsin/P</option> | 63 <option value="Chymotrypsin/P">Chymotrypsin/P</option> |
63 <option value="CNBr">CNBr</option> | 64 <option value="CNBr">CNBr</option> |
64 <option value="Formic_acid">Formic_acid</option> | 65 <option value="Formic_acid">Formic_acid</option> |
67 <option value="Lys-C/P">Lys-C/P</option> | 68 <option value="Lys-C/P">Lys-C/P</option> |
68 <option value="PepsinA">PepsinA</option> | 69 <option value="PepsinA">PepsinA</option> |
69 <option value="TrypChymo">TrypChymo</option> | 70 <option value="TrypChymo">TrypChymo</option> |
70 <option value="Trypsin/P">Trypsin/P</option> | 71 <option value="Trypsin/P">Trypsin/P</option> |
71 <option value="V8-DE">V8-DE</option> | 72 <option value="V8-DE">V8-DE</option> |
72 <option value="proline endopeptidase">proline endopeptidase</option> | |
73 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> | |
74 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> | |
75 <option value="no cleavage">no cleavage</option> | |
76 <option value="unspecific cleavage">unspecific cleavage</option> | |
77 <option value="Arg-C">Arg-C</option> | |
78 <option value="Arg-C/P">Arg-C/P</option> | |
79 <option value="Asp-N">Asp-N</option> | |
80 <option value="V8-E">V8-E</option> | 73 <option value="V8-E">V8-E</option> |
81 <option value="leukocyte elastase">leukocyte elastase</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> | |
82 <option value="Trypsin" selected="true">Trypsin</option> | 80 <option value="Trypsin" selected="true">Trypsin</option> |
83 <expand macro="list_string_san"/> | 81 <expand macro="list_string_san" name="enzyme"/> |
84 </param> | 82 </param> |
85 <param name="motif" argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help=""> | 83 <param argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help=""> |
86 <expand macro="list_string_san"/> | 84 <expand macro="list_string_san" name="motif"/> |
87 </param> | 85 </param> |
88 <expand macro="adv_opts_macro"> | 86 <expand macro="adv_opts_macro"> |
89 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 87 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
90 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 88 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
91 <expand macro="list_string_san"/> | 89 <expand macro="list_string_san" name="test"/> |
92 </param> | 90 </param> |
93 </expand> | 91 </expand> |
94 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 92 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
95 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
96 </param> | 94 </param> |
99 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> | 97 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> |
100 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 98 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
101 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 99 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
102 </data> | 100 </data> |
103 </outputs> | 101 </outputs> |
104 <tests> | 102 <tests/> |
105 <expand macro="autotest_DigestorMotif"/> | |
106 <expand macro="manutest_DigestorMotif"/> | |
107 </tests> | |
108 <help><![CDATA[digests a protein database in-silico | 103 <help><![CDATA[digests a protein database in-silico |
109 | 104 |
110 | 105 |
111 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DigestorMotif.html]]></help> | 106 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DigestorMotif.html]]></help> |
112 <expand macro="references"/> | 107 <expand macro="references"/> |
113 </tool> | 108 </tool> |