openms_spectrastsearchadapter: SpectraSTSearchAdapter.xml comparison

comparison SpectraSTSearchAdapter.xml @ 12:4d189842ebfc draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

author	galaxyp
date	Thu, 01 Dec 2022 19:03:12 +0000
parents	27ddea86fe90
children	52dd59548339

comparison

equal deleted inserted replaced

-:76adea1e0fde
+:4d189842ebfc
 <?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="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<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>
 <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token>
 <import>macros.xml</import>
-<import>macros_autotest.xml</import>
-<import>macros_test.xml</import>
 </macros>
 <expand macro="requirements"/>
 <expand macro="stdio"/>
 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
 @EXT_FOO@
 #import re
 ## Preprocessing
-mkdir spectra_files &&
+mkdir spectra_files_cond.spectra_files &&
-${ ' '.join(["ln -s '%s' 'spectra_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _]) }
+#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])}
+#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)' &&
+#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)' &&
 #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)' &&
 #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)' &&
 #end if
-#if $adv_opts_cond.adv_opts_selector=='advanced':
+#if $adv_opts.user_mod_file:
-#if $adv_opts_cond.user_mod_file:
+mkdir adv_opts.user_mod_file &&
-mkdir adv_opts_cond.user_mod_file &&
+ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' &&
-ln -s '$adv_opts_cond.user_mod_file' 'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)' &&
 #end if
-#end if
 ## Main program call
 set -o pipefail &&
 @EXECUTABLE@ -write_ctd ./ &&
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -spectra_files
-${' '.join(["'spectra_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])}
+#if $spectra_files_cond.spectra_files_select == "no"
+${' '.join(["'spectra_files_cond.spectra_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
+#else
+'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)'
+#end if
 -output_files
-${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $output_files_type) for _ in $spectra_files if _])}
+${' '.join(["'output_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $output_files_type) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
 -library_file
 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)'
 #if $sequence_database_file:
 -sequence_database_file
 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)'
 #end if
 #if $search_file:
 -search_file
 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)'
 #end if
-#if $adv_opts_cond.adv_opts_selector=='advanced':
+#if $adv_opts.user_mod_file:
-#if $adv_opts_cond.user_mod_file:
 -user_mod_file
-'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)'
+'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)'
 #end if
-#end if
 ## Postprocessing
-${' '.join(["&& mv -n 'output_files/%(id)s.%(omsext)s' 'output_files/%(id)s.%(gext)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for _ in $spectra_files if _])}
+${' '.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 $OPTIONAL_OUTPUTS
 && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
 <configfiles>
 <inputs name="args_json" data_style="paths"/>
 <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
 </configfiles>
 <inputs>
-<param name="spectra_files" 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)"/>
+<conditional name="spectra_files_cond">
+<param name="spectra_files_select" type="select" label="Run tool in batch mode for -spectra_files">
+<option value="no">No: process all datasets jointly</option>
+<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)"/>
+</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)"/>
+</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)">
 <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 name="library_file" 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" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
-<param name="sequence_database_file" argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta 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 name="sequence_database_type" argument="-sequence_database_type" display="radio" type="select" optional="false" label="Specify type of sequence database" help="">
+<param argument="-sequence_database_type" type="select" optional="true" label="Specify type of sequence database" help="">
 <option value="DNA">DNA</option>
 <option value="AA" selected="true">AA</option>
-<expand macro="list_string_san"/>
+<expand macro="list_string_san" name="sequence_database_type"/>
 </param>
-<param name="search_file" 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="-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 name="precursor_mz_tolerance" 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" 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"/>
 <expand macro="adv_opts_macro">
-<param name="use_isotopically_averaged_mass" 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_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
-<param name="use_all_charge_states" 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="-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 name="user_mod_file" argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
+<param argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
-<param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+<param 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="">
+<param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-<expand macro="list_string_san"/>
+<expand macro="list_string_san" name="test"/>
 </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>
 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
-<discover_datasets directory="output_files" pattern="__name_and_ext__"/>
+<discover_datasets directory="output_files" recurse="true" pattern="__name_and_ext__"/>
 </collection>
 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
 </data>
 </outputs>
-<tests>
+<tests><!-- TOPP_SpectrastSearchAdapter_1 -->
-<expand macro="autotest_SpectraSTSearchAdapter"/>
+<!-- TOPP_SpectrastSearchAdapter_2 -->
-<expand macro="manutest_SpectraSTSearchAdapter"/>
 </tests>
 <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
 <expand macro="references"/>
 </tool>

Mercurial > repos > galaxyp > openms_spectrastsearchadapter

comparison SpectraSTSearchAdapter.xml @ 12:4d189842ebfc draft