Mercurial > repos > galaxyp > openms_digestor

comparison Digestor.xml @ 14:13399dc8f687 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:09:26 +0000
parents 4827e132ac53
children 74db964d4818
comparison
equal deleted inserted replaced
13:28bc63599d10 14:13399dc8f687
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="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="Digestor" name="Digestor" 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@">Digestor</token> 7 <token name="@EXECUTABLE@">Digestor</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="input file" help=" select fasta data sets(s)"/> 42 <param argument="-in" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS"> 43 <param argument="-out_type" display="radio" type="select" optional="false" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
46 <option value="fasta">fasta</option> 44 <option value="fasta">fasta</option>
47 <option value="idXML">idxml</option> 45 <option value="idXML">idxml</option>
48 <expand macro="list_string_san"/> 46 <expand macro="list_string_san" name="out_type"/>
49 </param> 47 </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=""/> 48 <param 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=""/> 49 <param 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=""/> 50 <param 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=""> 51 <param argument="-enzyme" type="select" optional="true" label="The type of digestion enzyme" help="">
54 <option value="V8-E">V8-E</option> 52 <option value="Arg-C/P">Arg-C/P</option>
55 <option value="leukocyte elastase">leukocyte elastase</option> 53 <option value="Asp-N">Asp-N</option>
54 <option value="Asp-N/B">Asp-N/B</option>
55 <option value="Arg-C">Arg-C</option>
56 <option value="proline endopeptidase">proline endopeptidase</option> 56 <option value="proline endopeptidase">proline endopeptidase</option>
57 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 57 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
58 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 58 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
59 <option value="2-iodobenzoate">2-iodobenzoate</option> 59 <option value="no cleavage">no cleavage</option>
60 <option value="iodosobenzoate">iodosobenzoate</option> 60 <option value="unspecific cleavage">unspecific cleavage</option>
61 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
62 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 61 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
63 <option value="Glu-C+P">Glu-C+P</option> 62 <option value="Glu-C+P">Glu-C+P</option>
64 <option value="PepsinA + P">PepsinA + P</option> 63 <option value="PepsinA + P">PepsinA + P</option>
65 <option value="cyanogen-bromide">cyanogen-bromide</option> 64 <option value="cyanogen-bromide">cyanogen-bromide</option>
66 <option value="Clostripain/P">Clostripain/P</option> 65 <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> 66 <option value="Asp-N_ambic">Asp-N_ambic</option>
69 <option value="Chymotrypsin">Chymotrypsin</option> 67 <option value="Chymotrypsin">Chymotrypsin</option>
70 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 68 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
71 <option value="CNBr">CNBr</option> 69 <option value="CNBr">CNBr</option>
72 <option value="Formic_acid">Formic_acid</option> 70 <option value="Formic_acid">Formic_acid</option>
73 <option value="Lys-C">Lys-C</option> 71 <option value="Lys-C">Lys-C</option>
74 <option value="Lys-N">Lys-N</option> 72 <option value="Lys-N">Lys-N</option>
75 <option value="Lys-C/P">Lys-C/P</option> 73 <option value="Lys-C/P">Lys-C/P</option>
74 <option value="PepsinA">PepsinA</option>
75 <option value="TrypChymo">TrypChymo</option>
76 <option value="Trypsin/P">Trypsin/P</option> 76 <option value="Trypsin/P">Trypsin/P</option>
77 <option value="V8-DE">V8-DE</option> 77 <option value="V8-DE">V8-DE</option>
78 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> 78 <option value="V8-E">V8-E</option>
79 <option value="no cleavage">no cleavage</option> 79 <option value="leukocyte elastase">leukocyte elastase</option>
80 <option value="unspecific cleavage">unspecific cleavage</option> 80 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
81 <option value="Arg-C">Arg-C</option> 81 <option value="2-iodobenzoate">2-iodobenzoate</option>
82 <option value="Arg-C/P">Arg-C/P</option> 82 <option value="iodosobenzoate">iodosobenzoate</option>
83 <option value="Asp-N">Asp-N</option> 83 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
84 <option value="PepsinA">PepsinA</option>
85 <option value="TrypChymo">TrypChymo</option>
86 <option value="Trypsin" selected="true">Trypsin</option> 84 <option value="Trypsin" selected="true">Trypsin</option>
87 <expand macro="list_string_san"/> 85 <expand macro="list_string_san" name="enzyme"/>
88 </param> 86 </param>
89 <section name="FASTA" title="Options for FASTA output files" help="" expanded="false"> 87 <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=""> 88 <param name="ID" argument="-FASTA:ID" type="select" optional="true" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
91 <option value="parent" selected="true">parent</option> 89 <option value="parent" selected="true">parent</option>
92 <option value="number">number</option> 90 <option value="number">number</option>
93 <option value="both">both</option> 91 <option value="both">both</option>
94 <expand macro="list_string_san"/> 92 <expand macro="list_string_san" name="ID"/>
95 </param> 93 </param>
96 <param name="description" argument="-FASTA:description" display="radio" type="select" optional="false" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly"> 94 <param name="description" argument="-FASTA:description" type="select" optional="true" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
97 <option value="remove" selected="true">remove</option> 95 <option value="remove" selected="true">remove</option>
98 <option value="keep">keep</option> 96 <option value="keep">keep</option>
99 <expand macro="list_string_san"/> 97 <expand macro="list_string_san" name="description"/>
100 </param> 98 </param>
101 </section> 99 </section>
102 <expand macro="adv_opts_macro"> 100 <expand macro="adv_opts_macro">
103 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 101 <param 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=""> 102 <param 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"/> 103 <expand macro="list_string_san" name="test"/>
106 </param> 104 </param>
107 </expand> 105 </expand>
108 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 106 <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> 107 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
110 </param> 108 </param>
111 </inputs> 109 </inputs>
112 <outputs> 110 <outputs>
113 <data name="out" label="${tool.name} on ${on_string}: out"> 111 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta">
114 <change_format> 112 <change_format>
115 <when input="out_type" value="fasta" format="fasta"/>
116 <when input="out_type" value="idXML" format="idxml"/> 113 <when input="out_type" value="idXML" format="idxml"/>
117 </change_format> 114 </change_format>
118 </data> 115 </data>
119 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 116 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
120 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 117 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
121 </data> 118 </data>
122 </outputs> 119 </outputs>
123 <tests> 120 <tests><test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
124 <expand macro="autotest_Digestor"/> 121 <param name="adv_opts|test" value="true"/>
125 <expand macro="manutest_Digestor"/> 122 <param name="in" ftype="fasta" value="random.fa"/>
126 </tests> 123 <output name="out" ftype="fasta" value="Digestor.fasta"/>
124 <param name="out_type" value="fasta"/>
125 </test>
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/doxygen/release/2.6.0/html/UTILS_Digestor.html]]></help> 130 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Digestor.html]]></help>
131 <expand macro="references"/> 131 <expand macro="references"/>
132 </tool> 132 </tool>