Mercurial > repos > galaxyp > openms_digestormotif

comparison DigestorMotif.xml @ 10:bc7bd4710c4e 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 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:52:20 +0000
parents 861833218c65
children 01f5e95b5961
comparison
equal deleted inserted replaced
9:861833218c65 10:bc7bd4710c4e
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="2.3.0"> 4 <tool id="DigestorMotif" name="DigestorMotif" 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@">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>
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[DigestorMotif 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_missed_cleavages: 24
22 -missed_cleavages $param_missed_cleavages 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_mass_accuracy: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -mass_accuracy $param_mass_accuracy 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $param_min_length: 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 -min_length $param_min_length 31 -out
29 #end if 32 'out/output.${gxy2omsext("idxml")}'
30 #if $param_out_option: 33
31 -out_option $param_out_option 34 ## Postprocessing
32 #end if 35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
33 #if $param_enzyme: 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 -enzyme 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #if " " in str($param_enzyme): 38 #end if]]></command>
36 "$param_enzyme" 39 <configfiles>
37 #else 40 <inputs name="args_json" data_style="paths"/>
38 $param_enzyme 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #end if 42 </configfiles>
40 #end if
41 #if $param_motif:
42 -motif "$param_motif"
43 #end if
44 #if $adv_opts.adv_opts_selector=='advanced':
45 #if $adv_opts.param_force:
46 -force
47 #end if
48 #end if
49 ]]></command>
50 <inputs> 43 <inputs>
51 <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/>
52 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages) "/> 45 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/>
53 <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/> 46 <param name="mass_accuracy" argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/>
54 <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/> 47 <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/>
55 <param name="param_out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help="(-out_option) "/> 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=""/>
56 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) "> 49 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
57 <option value="Formic_acid">Formic_acid</option>
58 <option value="Alpha-lytic protease">Alpha-lytic protease</option> 50 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
59 <option value="V8-E">V8-E</option> 51 <option value="2-iodobenzoate">2-iodobenzoate</option>
60 <option value="unspecific cleavage">unspecific cleavage</option> 52 <option value="iodosobenzoate">iodosobenzoate</option>
61 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 53 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
62 <option value="V8-DE">V8-DE</option> 54 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
63 <option value="leukocyte elastase">leukocyte elastase</option> 55 <option value="Glu-C+P">Glu-C+P</option>
64 <option value="PepsinA">PepsinA</option> 56 <option value="PepsinA + P">PepsinA + P</option>
65 <option value="Arg-C">Arg-C</option> 57 <option value="cyanogen-bromide">cyanogen-bromide</option>
66 <option value="TrypChymo">TrypChymo</option> 58 <option value="Clostripain/P">Clostripain/P</option>
67 <option value="no cleavage">no cleavage</option> 59 <option value="Asp-N/B">Asp-N/B</option>
68 <option value="CNBr">CNBr</option> 60 <option value="Asp-N_ambic">Asp-N_ambic</option>
69 <option value="Trypsin/P">Trypsin/P</option>
70 <option value="Chymotrypsin">Chymotrypsin</option> 61 <option value="Chymotrypsin">Chymotrypsin</option>
71 <option value="Chymotrypsin/P">Chymotrypsin/P</option> 62 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
72 <option value="Asp-N_ambic">Asp-N_ambic</option> 63 <option value="CNBr">CNBr</option>
64 <option value="Formic_acid">Formic_acid</option>
73 <option value="Lys-C">Lys-C</option> 65 <option value="Lys-C">Lys-C</option>
66 <option value="Lys-N">Lys-N</option>
67 <option value="Lys-C/P">Lys-C/P</option>
68 <option value="PepsinA">PepsinA</option>
69 <option value="TrypChymo">TrypChymo</option>
70 <option value="Trypsin/P">Trypsin/P</option>
71 <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>
81 <option value="leukocyte elastase">leukocyte elastase</option>
74 <option value="Trypsin" selected="true">Trypsin</option> 82 <option value="Trypsin" selected="true">Trypsin</option>
75 <option value="Asp-N">Asp-N</option> 83 <expand macro="list_string_san"/>
76 <option value="Arg-C/P">Arg-C/P</option>
77 <option value="proline endopeptidase">proline endopeptidase</option>
78 <option value="Asp-N/B">Asp-N/B</option>
79 <option value="Lys-N">Lys-N</option>
80 <option value="2-iodobenzoate">2-iodobenzoate</option>
81 <option value="Lys-C/P">Lys-C/P</option>
82 </param> 84 </param>
83 <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) "> 85 <param name="motif" argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help="">
84 <sanitizer> 86 <expand macro="list_string_san"/>
85 <valid initial="string.printable">
86 <remove value="'"/>
87 <remove value="&quot;"/>
88 </valid>
89 </sanitizer>
90 </param> 87 </param>
91 <expand macro="advanced_options"> 88 <expand macro="adv_opts_macro">
92 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 89 <param name="force" 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="">
91 <expand macro="list_string_san"/>
92 </param>
93 </expand> 93 </expand>
94 <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>
96 </param>
94 </inputs> 97 </inputs>
95 <outputs> 98 <outputs>
96 <data name="param_out" format="idxml"/> 99 <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">
101 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
102 </data>
97 </outputs> 103 </outputs>
98 <help>digests a protein database in-silico 104 <tests>
105 <expand macro="autotest_DigestorMotif"/>
106 <expand macro="manutest_DigestorMotif"/>
107 </tests>
108 <help><![CDATA[digests a protein database in-silico
99 109
100 110
101 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_DigestorMotif.html</help> 111 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DigestorMotif.html]]></help>
112 <expand macro="references"/>
102 </tool> 113 </tool>