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comparison Digestor.xml @ 15:74db964d4818 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 21:36:14 +0000
parents 13399dc8f687
children
comparison
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14:13399dc8f687 15:74db964d4818
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="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="Digestor" name="Digestor" 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@">Digestor</token> 6 <token name="@EXECUTABLE@">Digestor</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
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="input file" help=" select fasta data sets(s)"/> 41 <param argument="-in" type="data" format="fasta" label="input file" help=" select fasta data sets(s)"/>
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"> 42 <param argument="-out_type" type="select" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
44 <option value="fasta">fasta</option> 43 <option value="fasta">fasta</option>
45 <option value="idXML">idxml</option> 44 <option value="idXML">idxml</option>
45 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
46 <expand macro="list_string_san" name="out_type"/> 46 <expand macro="list_string_san" name="out_type"/>
47 </param> 47 </param>
48 <param 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" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
49 <param argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/> 49 <param argument="-min_length" type="integer" value="6" label="Minimum length of peptide" help=""/>
50 <param argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/> 50 <param argument="-max_length" type="integer" value="40" label="Maximum length of peptide" help=""/>
51 <param argument="-enzyme" type="select" optional="true" label="The type of digestion enzyme" help=""> 51 <param argument="-enzyme" type="select" label="The type of digestion enzyme" help="">
52 <option value="Arg-C/P">Arg-C/P</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>
57 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
58 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
59 <option value="no cleavage">no cleavage</option> 52 <option value="no cleavage">no cleavage</option>
60 <option value="unspecific cleavage">unspecific cleavage</option> 53 <option value="unspecific cleavage">unspecific cleavage</option>
54 <option value="V8-DE">V8-DE</option>
55 <option value="V8-E">V8-E</option>
56 <option value="leukocyte elastase">leukocyte elastase</option>
57 <option value="proline endopeptidase">proline endopeptidase</option>
58 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
61 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> 59 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
62 <option value="Glu-C+P">Glu-C+P</option> 60 <option value="Glu-C+P">Glu-C+P</option>
63 <option value="PepsinA + P">PepsinA + P</option> 61 <option value="PepsinA + P">PepsinA + P</option>
64 <option value="cyanogen-bromide">cyanogen-bromide</option> 62 <option value="cyanogen-bromide">cyanogen-bromide</option>
65 <option value="Clostripain/P">Clostripain/P</option> 63 <option value="Clostripain/P">Clostripain/P</option>
64 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
65 <option value="TrypChymo">TrypChymo</option>
66 <option value="Trypsin/P">Trypsin/P</option>
67 <option value="Trypsin" selected="true">Trypsin</option>
68 <option value="Arg-C">Arg-C</option>
69 <option value="Arg-C/P">Arg-C/P</option>
70 <option value="Asp-N">Asp-N</option>
71 <option value="Asp-N/B">Asp-N/B</option>
66 <option value="Asp-N_ambic">Asp-N_ambic</option> 72 <option value="Asp-N_ambic">Asp-N_ambic</option>
67 <option value="Chymotrypsin">Chymotrypsin</option> 73 <option value="Chymotrypsin">Chymotrypsin</option>
68 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 74 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
69 <option value="CNBr">CNBr</option> 75 <option value="CNBr">CNBr</option>
70 <option value="Formic_acid">Formic_acid</option> 76 <option value="Formic_acid">Formic_acid</option>
71 <option value="Lys-C">Lys-C</option> 77 <option value="Lys-C">Lys-C</option>
72 <option value="Lys-N">Lys-N</option> 78 <option value="Lys-N">Lys-N</option>
73 <option value="Lys-C/P">Lys-C/P</option> 79 <option value="Lys-C/P">Lys-C/P</option>
74 <option value="PepsinA">PepsinA</option> 80 <option value="PepsinA">PepsinA</option>
75 <option value="TrypChymo">TrypChymo</option> 81 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
76 <option value="Trypsin/P">Trypsin/P</option>
77 <option value="V8-DE">V8-DE</option>
78 <option value="V8-E">V8-E</option>
79 <option value="leukocyte elastase">leukocyte elastase</option>
80 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 82 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
81 <option value="2-iodobenzoate">2-iodobenzoate</option> 83 <option value="2-iodobenzoate">2-iodobenzoate</option>
82 <option value="iodosobenzoate">iodosobenzoate</option> 84 <option value="iodosobenzoate">iodosobenzoate</option>
83 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
84 <option value="Trypsin" selected="true">Trypsin</option>
85 <expand macro="list_string_san" name="enzyme"/> 85 <expand macro="list_string_san" name="enzyme"/>
86 </param> 86 </param>
87 <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">
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=""> 88 <param name="ID" argument="-FASTA:ID" type="select" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
89 <option value="parent" selected="true">parent</option> 89 <option value="parent" selected="true">parent</option>
90 <option value="number">number</option> 90 <option value="number">number</option>
91 <option value="both">both</option> 91 <option value="both">both</option>
92 <expand macro="list_string_san" name="ID"/> 92 <expand macro="list_string_san" name="ID"/>
93 </param> 93 </param>
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"> 94 <param name="description" argument="-FASTA:description" type="select" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
95 <option value="remove" selected="true">remove</option> 95 <option value="remove" selected="true">remove</option>
96 <option value="keep">keep</option> 96 <option value="keep">keep</option>
97 <expand macro="list_string_san" name="description"/> 97 <expand macro="list_string_san" name="description"/>
98 </param> 98 </param>
99 </section> 99 </section>
100 <expand macro="adv_opts_macro"> 100 <expand macro="adv_opts_macro">
101 <param 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=""/>
102 <param 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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
103 <expand macro="list_string_san" name="test"/> 103 <expand macro="list_string_san" name="test"/>
104 </param> 104 </param>
105 </expand> 105 </expand>
106 <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">
107 <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>
115 </data> 115 </data>
116 <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">
117 <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>
118 </data> 118 </data>
119 </outputs> 119 </outputs>
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 --> 120 <tests>
121 <param name="adv_opts|test" value="true"/> 121 <test expect_num_outputs="1">
122 <param name="in" ftype="fasta" value="random.fa"/> 122 <!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
123 <output name="out" ftype="fasta" value="Digestor.fasta"/> 123 <param name="adv_opts|test" value="true"/>
124 <param name="out_type" value="fasta"/> 124 <param name="in" ftype="fasta" value="random.fa"/>
125 </test> 125 <output name="out" ftype="fasta" value="Digestor.fasta"/>
126 </tests> 126 <param name="out_type" value="fasta"/>
127 </test>
128 </tests>
127 <help><![CDATA[Digests a protein database in-silico. 129 <help><![CDATA[Digests a protein database in-silico.
128 130
129 131
130 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Digestor.html]]></help> 132 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_Digestor.html]]></help>
131 <expand macro="references"/> 133 <expand macro="references"/>
132 </tool> 134 </tool>