Mercurial > repos > galaxyp > openms_databasesuitability
diff DatabaseSuitability.xml @ 3:2470b498fc12 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:46:31 +0000 |
| parents | 4890f50ae1a2 |
| children |
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--- a/DatabaseSuitability.xml Thu Dec 01 19:02:20 2022 +0000 +++ b/DatabaseSuitability.xml Fri Jun 14 21:46:31 2024 +0000 @@ -1,8 +1,7 @@ -<?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: [Quality Control]--> <tool id="DatabaseSuitability" name="DatabaseSuitability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.</description> + <description>Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra</description> <macros> <token name="@EXECUTABLE@">DatabaseSuitability</token> <import>macros.xml</import> @@ -15,15 +14,15 @@ ## Preprocessing mkdir in_id && -ln -s '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' && +cp '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' && mkdir in_spec && -ln -s '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' && +cp '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' && mkdir in_novo && -ln -s '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' && +cp '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && mkdir novo_database && -ln -s '$novo_database' 'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)' && +cp '$novo_database' 'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if @@ -64,24 +63,24 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in_id" type="data" format="idxml" optional="false" label="Input idXML file from a peptide identification search with a combined database" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/> - <param argument="-in_spec" type="data" format="mzml" optional="false" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/> - <param argument="-in_novo" type="data" format="idxml" optional="false" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/> - <param argument="-database" type="data" format="fasta" optional="false" label="Input FASTA file of the database in question" help=" select fasta data sets(s)"/> - <param argument="-novo_database" type="data" format="fasta" optional="false" label="Input deNovo sequences derived from MzML given in 'in_spec' concatenated to one FASTA entry" help=" select fasta data sets(s)"/> + <param argument="-in_id" type="data" format="idxml" label="Input idXML file from a peptide identification search with a combined database" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/> + <param argument="-in_spec" type="data" format="mzml" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/> + <param argument="-in_novo" type="data" format="idxml" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/> + <param argument="-database" type="data" format="fasta" label="Input FASTA file of the database in question" help=" select fasta data sets(s)"/> + <param argument="-novo_database" type="data" format="fasta" label="Input deNovo sequences derived from MzML given in 'in_spec' concatenated to one FASTA entry" help=" select fasta data sets(s)"/> <section name="algorithm" title="Parameter section for the suitability calculation algorithm" help="" expanded="false"> <param name="no_rerank" argument="-algorithm:no_rerank" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if you want to disable re-ranking" help="Cases, where a de novo peptide scores just higher than the database peptide, are overlooked and counted as a de novo hit. This might underestimate the database quality"/> - <param name="reranking_cutoff_percentile" argument="-algorithm:reranking_cutoff_percentile" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM" help="The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top"/> - <param name="FDR" argument="-algorithm:FDR" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Filter peptide hits based on this q-value" help="(e.g., 0.05 = 5 % FDR)"/> - <param name="number_of_subsampled_runs" argument="-algorithm:number_of_subsampled_runs" type="integer" optional="true" min="0" value="1" label="Controls how many runs should be done for calculating corrected suitability" help="(0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time"/> + <param name="reranking_cutoff_percentile" argument="-algorithm:reranking_cutoff_percentile" type="float" min="0.0" max="1.0" value="0.01" label="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM" help="The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top"/> + <param name="FDR" argument="-algorithm:FDR" type="float" min="0.0" max="1.0" value="0.01" label="Filter peptide hits based on this q-value" help="(e.g., 0.05 = 5 % FDR)"/> + <param name="number_of_subsampled_runs" argument="-algorithm:number_of_subsampled_runs" type="integer" min="0" value="1" label="Controls how many runs should be done for calculating corrected suitability" help="(0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time"/> <param name="keep_search_files" argument="-algorithm:keep_search_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you wish to keep the files used by and produced by the internal ID search" help=""/> <param name="disable_correction" argument="-algorithm:disable_correction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to disable the calculation of the corrected suitability" help=""/> <param name="force" argument="-algorithm:force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to enforce re-ranking when no cross correlation score is present" help="For re-ranking the default score found at each peptide hit is used. Use with care!"/> </section> <expand macro="adv_opts_macro"> - <param argument="-novo_threshold" type="float" optional="true" min="0.0" value="60.0" label="Minimum score a de novo sequence has to have to be defined as 'correct'" help="The default of 60 is proven to be a good estimate for sequences generated by Novor"/> + <param argument="-novo_threshold" type="float" min="0.0" value="60.0" label="Minimum score a de novo sequence has to have to be defined as 'correct'" help="The default of 60 is proven to be a good estimate for sequences generated by Novor"/> <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> @@ -101,7 +100,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_DatabaseSuitability_1 --> + <tests> + <!-- TOPP_DatabaseSuitability --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="novo_threshold" value="60.0"/> @@ -113,7 +113,39 @@ <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> <param name="database" value="DatabaseSuitability_database.fasta"/> <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/> - <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="DatabaseSuitability_out.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <section name="algorithm"> + <param name="no_rerank" value="false"/> + <param name="reranking_cutoff_percentile" value="0.01"/> + <param name="FDR" value="0.01"/> + <param name="number_of_subsampled_runs" value="1"/> + <param name="keep_search_files" value="false"/> + <param name="disable_correction" value="true"/> + <param name="force" value="false"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> + </test> + <!-- TOPP_DatabaseSuitability_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="novo_threshold" value="60.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> + <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> + <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> + <param name="database" value="DatabaseSuitability_database.fasta"/> + <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/> + <output name="out" value="DatabaseSuitability_out_1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <section name="algorithm"> <param name="no_rerank" value="false"/> <param name="reranking_cutoff_percentile" value="0.01"/> @@ -129,6 +161,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_DatabaseSuitability_2 --> <test expect_num_outputs="2"> @@ -142,7 +177,7 @@ <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> <param name="database" value="DatabaseSuitability_database.fasta"/> <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/> - <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="DatabaseSuitability_out_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <section name="algorithm"> <param name="no_rerank" value="false"/> <param name="reranking_cutoff_percentile" value="0.01"/> @@ -158,6 +193,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_DatabaseSuitability_3 --> <test expect_num_outputs="2"> @@ -171,7 +209,7 @@ <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> <param name="database" value="DatabaseSuitability_database.fasta"/> <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/> - <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="DatabaseSuitability_out_3.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <section name="algorithm"> <param name="no_rerank" value="false"/> <param name="reranking_cutoff_percentile" value="0.5"/> @@ -187,11 +225,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DatabaseSuitability.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DatabaseSuitability.html]]></help> <expand macro="references"/> </tool>