Mercurial > repos > galaxyp > openms_digestormotif
diff DigestorMotif.xml @ 13:38106b5b3bc6 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 18:19:48 +0000 |
| parents | 661cb880129a |
| children |
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--- a/DigestorMotif.xml Wed May 15 06:56:13 2019 -0400 +++ b/DigestorMotif.xml Tue Oct 13 18:19:48 2020 +0000 @@ -1,102 +1,113 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Utilities]--> -<tool id="DigestorMotif" name="DigestorMotif" version="2.3.0"> +<tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>digests a protein database in-silico</description> <macros> <token name="@EXECUTABLE@">DigestorMotif</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[DigestorMotif + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-out +'out/output.${gxy2omsext("idxml")}' -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_missed_cleavages: - -missed_cleavages $param_missed_cleavages -#end if -#if $param_mass_accuracy: - -mass_accuracy $param_mass_accuracy -#end if -#if $param_min_length: - -min_length $param_min_length -#end if -#if $param_out_option: - -out_option $param_out_option -#end if -#if $param_enzyme: - -enzyme - #if " " in str($param_enzyme): - "$param_enzyme" - #else - $param_enzyme - #end if -#end if -#if $param_motif: - -motif "$param_motif" -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${gxy2omsext("idxml")}' '$out' +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in) "/> - <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages) "/> - <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/> - <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/> - <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) "/> - <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) "> - <option value="Formic_acid">Formic_acid</option> + <param name="in" argument="-in" type="data" format="fasta" optional="false" label="FASTA input file" help=" select fasta data sets(s)"/> + <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="the number of allowed missed cleavages" help=""/> + <param name="mass_accuracy" argument="-mass_accuracy" type="integer" optional="true" value="1000" label="give your mass accuracy in pp" help=""/> + <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="minimum length of peptide" help=""/> + <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=""/> + <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="V8-E">V8-E</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="V8-DE">V8-DE</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="PepsinA">PepsinA</option> - <option value="Arg-C">Arg-C</option> - <option value="TrypChymo">TrypChymo</option> - <option value="no cleavage">no cleavage</option> - <option value="CNBr">CNBr</option> - <option value="Trypsin/P">Trypsin/P</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> + <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> + <option value="Glu-C+P">Glu-C+P</option> + <option value="PepsinA + P">PepsinA + P</option> + <option value="cyanogen-bromide">cyanogen-bromide</option> + <option value="Clostripain/P">Clostripain/P</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="Chymotrypsin">Chymotrypsin</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> <option value="Lys-C">Lys-C</option> - <option value="Trypsin" selected="true">Trypsin</option> - <option value="Asp-N">Asp-N</option> + <option value="Lys-N">Lys-N</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Arg-C">Arg-C</option> <option value="Arg-C/P">Arg-C/P</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Lys-N">Lys-N</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="Lys-C/P">Lys-C/P</option> + <option value="Asp-N">Asp-N</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="Trypsin" selected="true">Trypsin</option> + <expand macro="list_string_san"/> </param> - <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="motif" argument="-motif" type="text" optional="true" value="M" label="the motif for the restricted peptidome" help=""> + <expand macro="list_string_san"/> </param> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="idxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>digests a protein database in-silico + <tests> + <expand macro="autotest_DigestorMotif"/> + <expand macro="manutest_DigestorMotif"/> + </tests> + <help><![CDATA[digests a protein database in-silico -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_DigestorMotif.html</help> +For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DigestorMotif.html]]></help> + <expand macro="references"/> </tool>