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comparison Digestor.xml @ 10:7af5860ae563 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:23:17 +0000
parents 688f329e6583
children 4827e132ac53
comparison
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9:688f329e6583 10:7af5860ae563
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="2.3.0"> 4 <tool id="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[Digestor 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_out_type: 24
22 -out_type 25 set -o pipefail &&
23 #if " " in str($param_out_type): 26 @EXECUTABLE@ -write_ctd ./ &&
24 "$param_out_type" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 $param_out_type 29 -in
27 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 31 -out
29 #if $param_missed_cleavages: 32 'out/output.${out_type}'
30 -missed_cleavages $param_missed_cleavages 33
31 #end if 34 ## Postprocessing
32 #if $param_min_length: 35 && mv 'out/output.${out_type}' '$out'
33 -min_length $param_min_length 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #if $param_max_length: 38 #end if]]></command>
36 -max_length $param_max_length 39 <configfiles>
37 #end if 40 <inputs name="args_json" data_style="paths"/>
38 #if $param_enzyme: 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 -enzyme 42 </configfiles>
40 #if " " in str($param_enzyme):
41 "$param_enzyme"
42 #else
43 $param_enzyme
44 #end if
45 #end if
46 #if $adv_opts.adv_opts_selector=='advanced':
47 #if $adv_opts.param_force:
48 -force
49 #end if
50 #end if
51 ]]></command>
52 <inputs> 43 <inputs>
53 <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
54 <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"> 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">
55 <option value="idXML">idXML</option>
56 <option value="fasta">fasta</option> 46 <option value="fasta">fasta</option>
47 <option value="idXML">idxml</option>
48 <expand macro="list_string_san"/>
57 </param> 49 </param>
58 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages) "/> 50 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
59 <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length) "/> 51 <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/>
60 <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length) "/> 52 <param name="max_length" argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/>
61 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme) "> 53 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The type of digestion enzyme" help="">
54 <option value="Asp-N">Asp-N</option>
55 <option value="Asp-N/B">Asp-N/B</option>
56 <option value="Asp-N_ambic">Asp-N_ambic</option>
57 <option value="cyanogen-bromide">cyanogen-bromide</option>
58 <option value="Clostripain/P">Clostripain/P</option>
59 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
60 <option value="no cleavage">no cleavage</option>
61 <option value="unspecific cleavage">unspecific cleavage</option>
62 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
63 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
64 <option value="Glu-C+P">Glu-C+P</option>
65 <option value="PepsinA + P">PepsinA + P</option>
66 <option value="leukocyte elastase">leukocyte elastase</option>
62 <option value="proline endopeptidase">proline endopeptidase</option> 67 <option value="proline endopeptidase">proline endopeptidase</option>
63 <option value="V8-DE">V8-DE</option>
64 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
65 <option value="no cleavage">no cleavage</option>
66 <option value="2-iodobenzoate">2-iodobenzoate</option>
67 <option value="leukocyte elastase">leukocyte elastase</option>
68 <option value="V8-E">V8-E</option>
69 <option value="unspecific cleavage">unspecific cleavage</option>
70 <option value="Arg-C">Arg-C</option>
71 <option value="CNBr">CNBr</option>
72 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
73 <option value="Chymotrypsin">Chymotrypsin</option> 68 <option value="Chymotrypsin">Chymotrypsin</option>
74 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 69 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
70 <option value="CNBr">CNBr</option>
71 <option value="Formic_acid">Formic_acid</option>
72 <option value="Lys-C">Lys-C</option>
73 <option value="Lys-N">Lys-N</option>
74 <option value="Lys-C/P">Lys-C/P</option>
75 <option value="PepsinA">PepsinA</option>
75 <option value="TrypChymo">TrypChymo</option> 76 <option value="TrypChymo">TrypChymo</option>
76 <option value="Asp-N_ambic">Asp-N_ambic</option> 77 <option value="Trypsin/P">Trypsin/P</option>
77 <option value="Lys-C">Lys-C</option> 78 <option value="V8-DE">V8-DE</option>
79 <option value="V8-E">V8-E</option>
80 <option value="Arg-C">Arg-C</option>
81 <option value="Arg-C/P">Arg-C/P</option>
82 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
83 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
84 <option value="2-iodobenzoate">2-iodobenzoate</option>
85 <option value="iodosobenzoate">iodosobenzoate</option>
78 <option value="Trypsin" selected="true">Trypsin</option> 86 <option value="Trypsin" selected="true">Trypsin</option>
79 <option value="Trypsin/P">Trypsin/P</option> 87 <expand macro="list_string_san"/>
80 <option value="Asp-N">Asp-N</option>
81 <option value="Lys-N">Lys-N</option>
82 <option value="Formic_acid">Formic_acid</option>
83 <option value="Lys-C/P">Lys-C/P</option>
84 <option value="Asp-N/B">Asp-N/B</option>
85 <option value="PepsinA">PepsinA</option>
86 <option value="Arg-C/P">Arg-C/P</option>
87 </param> 88 </param>
88 <expand macro="advanced_options"> 89 <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
89 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 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="">
91 <option value="parent" selected="true">parent</option>
92 <option value="number">number</option>
93 <option value="both">both</option>
94 <expand macro="list_string_san"/>
95 </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">
97 <option value="remove" selected="true">remove</option>
98 <option value="keep">keep</option>
99 <expand macro="list_string_san"/>
100 </param>
101 </section>
102 <expand macro="adv_opts_macro">
103 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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="">
105 <expand macro="list_string_san"/>
106 </param>
90 </expand> 107 </expand>
108 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
110 </param>
91 </inputs> 111 </inputs>
92 <outputs> 112 <outputs>
93 <data name="param_out" format="fasta"/> 113 <data name="out" label="${tool.name} on ${on_string}: out">
114 <change_format>
115 <when input="out_type" value="fasta" format="fasta"/>
116 <when input="out_type" value="idXML" format="idxml"/>
117 </change_format>
118 </data>
119 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
120 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
121 </data>
94 </outputs> 122 </outputs>
95 <help>Digests a protein database in-silico. 123 <tests>
124 <expand macro="autotest_Digestor"/>
125 <expand macro="manutest_Digestor"/>
126 </tests>
127 <help><![CDATA[Digests a protein database in-silico.
96 128
97 129
98 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_Digestor.html</help> 130 For more information, visit http://www.openms.de/documentation/UTILS_Digestor.html]]></help>
131 <expand macro="references"/>
99 </tool> 132 </tool>