Mercurial > repos > galaxyp > openms_spectrastsearchadapter
diff SpectraSTSearchAdapter.xml @ 13:52dd59548339 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:34:58 +0000 |
parents | 4d189842ebfc |
children |
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--- a/SpectraSTSearchAdapter.xml Thu Dec 01 19:03:12 2022 +0000 +++ b/SpectraSTSearchAdapter.xml Fri Jun 14 21:34:58 2024 +0000 @@ -1,6 +1,5 @@ -<?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]--> +<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]--> <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Interface to the SEARCH Mode of the SpectraST executable</description> <macros> @@ -17,27 +16,29 @@ mkdir spectra_files_cond.spectra_files && #if $spectra_files_cond.spectra_files_select == "no" mkdir ${' '.join(["'spectra_files_cond.spectra_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && -${' '.join(["ln -s '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} +${' '.join(["cp '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} #else -ln -s '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' && +cp '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' && #end if mkdir output_files && mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && mkdir library_file && -ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' && +cp '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' && #if $sequence_database_file: mkdir sequence_database_file && - ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' && + cp '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' && #end if #if $search_file: mkdir search_file && - ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' && + cp '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' && #end if +## advanced options #if $adv_opts.user_mod_file: mkdir adv_opts.user_mod_file && - ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' && + cp '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' && #end if + ## Main program call set -o pipefail && @@ -62,11 +63,13 @@ -search_file 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' #end if +## advanced options #if $adv_opts.user_mod_file: -user_mod_file 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' #end if + ## Postprocessing ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn)s/%(id)s.%(gext)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for i, f in enumerate($spectra_files_cond.spectra_files) if f])} #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS @@ -83,34 +86,34 @@ <option value="yes">Yes: process each dataset in an independent job</option> </param> <when value="no"> - <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/> + <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/> </when> <when value="yes"> - <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="false" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/> + <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/> </when> </conditional> - <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)"> + <param name="output_files_type" type="select" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)"> <option value="txt">txt</option> <option value="tsv">tabular (tsv)</option> <option value="pep.xml">pepxml (pep.xml)</option> <option value="pepXML">pepxml</option> <option value="html">html</option> </param> - <param argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/> + <param argument="-library_file" type="data" format="splib" label="Specify library file" help=" select splib data sets(s)"/> <param argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/> - <param argument="-sequence_database_type" type="select" optional="true" label="Specify type of sequence database" help=""> + <param argument="-sequence_database_type" type="select" label="Specify type of sequence database" help=""> <option value="DNA">DNA</option> <option value="AA" selected="true">AA</option> <expand macro="list_string_san" name="sequence_database_type"/> </param> <param argument="-search_file" type="data" format="txt" optional="true" label="Only search a subset of the query spectra in the search file" help=" select txt data sets(s)"/> - <param argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/> + <param argument="-precursor_mz_tolerance" type="float" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/> <expand macro="adv_opts_macro"> <param argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/> <param argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/> <param argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is "spectrast.usermods" select txt data sets(s)"/> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -126,12 +129,13 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_SpectrastSearchAdapter_1 --> + <tests> + <!-- TOPP_SpectrastSearchAdapter_1 --> <!-- TOPP_SpectrastSearchAdapter_2 --> </tests> <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraSTSearchAdapter.html]]></help> <expand macro="references"/> </tool>