Mercurial > repos > galaxyp > openms_speclibsearcher
diff SpecLibSearcher.xml @ 8:3aa3b656e624 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:12:08 +0000 |
parents | 863a35a84426 |
children | 2d6e49acbb56 |
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--- a/SpecLibSearcher.xml Fri Nov 06 20:40:25 2020 +0000 +++ b/SpecLibSearcher.xml Thu Dec 01 19:12:08 2022 +0000 @@ -1,13 +1,11 @@ <?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: [Identification]--> -<tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</description> <macros> <token name="@EXECUTABLE@">SpecLibSearcher</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -16,11 +14,17 @@ #import re ## Preprocessing -mkdir in && -${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir in_cond.in && +#if $in_cond.in_select == "no" +mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && +${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +#else +ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +#end if mkdir lib && ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && mkdir out && +mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && ## Main program call @@ -29,14 +33,18 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in -${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +#if $in_cond.in_select == "no" +${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +#else +'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' +#end if -lib 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' -out -${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("idxml")) for _ in $in if _])} +${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("idxml")) for i, f in enumerate($in_cond.in) if f])} ## Postprocessing -${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("idxml")} for _ in $out if _])} +${' '.join(["&& mv -n 'out/%(bn)s/%(id)s.%(gext)s' 'out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("idxml")} for i, f in enumerate($in_cond.in) if f])} #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' #end if]]></command> @@ -45,28 +53,39 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/> - <param name="lib" argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/> - <param name="compare_function" argument="-compare_function" type="select" optional="false" label="function for similarity comparison" help=""> + <conditional name="in_cond"> + <param name="in_select" type="select" label="Run tool in batch mode for -in"> + <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="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/> + </when> + <when value="yes"> + <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files" help=" select mzml data sets(s)"/> + </when> + </conditional> + <param argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/> + <param argument="-compare_function" type="select" optional="true" label="function for similarity comparison" help=""> <option value="PeakAlignment">PeakAlignment</option> <option value="SpectrumAlignmentScore">SpectrumAlignmentScore</option> <option value="SpectrumCheapDPCorr">SpectrumCheapDPCorr</option> <option value="SpectrumPrecursorComparator">SpectrumPrecursorComparator</option> <option value="SteinScottImproveScore">SteinScottImproveScore</option> <option value="ZhangSimilarityScore" selected="true">ZhangSimilarityScore</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="compare_function"/> </param> <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> - <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> + <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mass_tolerance_unit"/> </param> <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_integer_valsan"/> + <expand macro="list_integer_valsan" name="isotopes"/> </param> </section> <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> @@ -83,7 +102,6 @@ </section> <section name="modifications" title="Modifications Options" help="" expanded="false"> <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> - <option value="">default (nothing chosen)</option> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -1453,7 +1471,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> @@ -3012,10 +3029,9 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fixed"/> </param> <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'"> - <option value="">default (nothing chosen)</option> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -4385,7 +4401,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> @@ -5944,14 +5959,14 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="variable"/> </param> <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/> </section> <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 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=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -5960,19 +5975,59 @@ </inputs> <outputs> <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> - <discover_datasets directory="out" format="idxml" pattern="__name__"/> + <discover_datasets directory="out" recurse="true" format="idxml" pattern="__name__"/> </collection> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_SpecLibSearcher"/> - <expand macro="manutest_SpecLibSearcher"/> + <tests><!-- TOPP_SpecLibSearcher_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <conditional name="in_cond"> + <param name="in" value="SpecLibSearcher_1.mzML"/> + </conditional> + <param name="lib" value="SpecLibSearcher_1.MSP"/> + <output_collection name="out" count="1"/> + <param name="compare_function" value="ZhangSimilarityScore"/> + <section name="precursor"> + <param name="mass_tolerance" value="3.0"/> + <param name="mass_tolerance_unit" value="Da"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="10.0"/> + </section> + <section name="report"> + <param name="top_hits" value="10"/> + </section> + <section name="filter"> + <param name="remove_peaks_below_threshold" value="2.01"/> + <param name="min_peaks" value="5"/> + <param name="max_peaks" value="150"/> + <param name="cut_peaks_below" value="1000"/> + </section> + <section name="modifications"> + <param name="fixed"/> + <param name="variable"/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpecLibSearcher.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpecLibSearcher.html]]></help> <expand macro="references"/> </tool>