Mercurial > repos > galaxyp > openms_proteinquantifier
diff ProteinQuantifier.xml @ 14:89ece0562fe0 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 21:34:51 +0000 |
| parents | d426affe977c |
| children |
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--- a/ProteinQuantifier.xml Thu Dec 01 19:18:55 2022 +0000 +++ b/ProteinQuantifier.xml Fri Jun 14 21:34:51 2024 +0000 @@ -1,4 +1,3 @@ -<?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: [Quantitation]--> <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> @@ -15,14 +14,14 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $protein_groups: mkdir protein_groups && - ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' && + cp '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' && #end if #if $design: mkdir design && - ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && + cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && @@ -84,43 +83,50 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> - <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/> + <param argument="-in" type="data" format="consensusxml,featurexml,idxml" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> + <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. via the ProteinInference tool).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/> <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> - <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/> - <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help=""> - <option value="median" selected="true">median</option> - <option value="mean">mean</option> - <option value="weighted_mean">weighted_mean</option> - <option value="sum">sum</option> - <expand macro="list_string_san" name="average"/> + <param argument="-method" type="select" label="- top - quantify based on three most abundant peptides (number can be changed in 'top')" help="- iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!"> + <option value="top" selected="true">top</option> + <option value="iBAQ">iBAQ</option> + <expand macro="list_string_san" name="method"/> </param> - <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/> <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/> <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/> <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) "/> <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)"/> + <section name="top" title="Additional options for custom quantification using top N peptides" help="" expanded="false"> + <param name="N" argument="-top:N" type="integer" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/> + <param name="aggregate" argument="-top:aggregate" type="select" label="Aggregation method used to compute protein abundances from peptide abundances" help=""> + <option value="median" selected="true">median</option> + <option value="mean">mean</option> + <option value="weighted_mean">weighted_mean</option> + <option value="sum">sum</option> + <expand macro="list_string_san" name="aggregate"/> + </param> + <param name="include_all" argument="-top:include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'N' (no effect if 'N' is 0 or 1)" help=""/> + </section> <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false"> <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/> - <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> + <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'N 0',all peptides that occur in every sample are considered.. Otherwise ('N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> </section> <section name="format" title="Output formatting options" help="" expanded="false"> <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help=""> <expand macro="list_string_san" name="separator"/> </param> - <param name="quoting" argument="-format:quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> + <param name="quoting" argument="-format:quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> <option value="none">none</option> <option value="double" selected="true">double</option> <option value="escape">escape</option> <expand macro="list_string_san" name="quoting"/> </param> - <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help=""> + <param name="replacement" argument="-format:replacement" type="text" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help=""> <expand macro="list_string_san" name="replacement"/> </param> </section> <expand macro="adv_opts_macro"> <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> @@ -148,22 +154,26 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_ProteinQuantifier_1 --> + <tests> + <!-- TOPP_ProteinQuantifier_1 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="median"/> - <param name="include_all" value="false"/> + <output name="out" value="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" value="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="median"/> + <param name="include_all" value="false"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="false"/> @@ -179,6 +189,9 @@ <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_ProteinQuantifier_2 --> <test expect_num_outputs="3"> @@ -187,15 +200,18 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> + <output name="out" value="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" value="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="true"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="2"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="true"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="false"/> @@ -211,6 +227,9 @@ <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_ProteinQuantifier_3 --> <test expect_num_outputs="3"> @@ -219,15 +238,18 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_3_input.featureXML"/> - <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="mean"/> - <param name="include_all" value="true"/> + <output name="out" value="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" value="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="2"/> + <param name="aggregate" value="mean"/> + <param name="include_all" value="true"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="false"/> @@ -243,6 +265,9 @@ <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_ProteinQuantifier_4 --> <test expect_num_outputs="2"> @@ -251,14 +276,17 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> + <output name="out" value="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="0"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="false"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="false"/> @@ -274,6 +302,9 @@ <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_ProteinQuantifier_5 --> <test expect_num_outputs="2"> @@ -282,14 +313,17 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> + <output name="out" value="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="false"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="false"/> @@ -305,6 +339,9 @@ <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_ProteinQuantifier_6 --> <test expect_num_outputs="2"> @@ -313,14 +350,17 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> + <output name="out" value="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="true"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="false"/> @@ -336,6 +376,9 @@ <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_ProteinQuantifier_7 --> <test expect_num_outputs="2"> @@ -344,14 +387,17 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> + <output name="out" value="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="0"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="false"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="true"/> @@ -367,6 +413,9 @@ <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_ProteinQuantifier_8 --> <test expect_num_outputs="2"> @@ -375,14 +424,17 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> + <output name="out" value="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="false"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="true"/> @@ -398,6 +450,9 @@ <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_ProteinQuantifier_9 --> <test expect_num_outputs="3"> @@ -406,15 +461,18 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> + <output name="out" value="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="mztab" value="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="true"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="true"/> @@ -430,6 +488,9 @@ <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_ProteinQuantifier_12 --> <test expect_num_outputs="2"> @@ -438,14 +499,54 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> + <output name="out" value="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="true"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="true"/> + </section> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </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_ProteinQuantifier_13 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" value="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="true"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="true"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="true"/> @@ -461,37 +562,9 @@ <is_valid_xml/> </assert_contents> </output> - </test> - <!-- TOPP_ProteinQuantifier_13 --> - <test expect_num_outputs="2"> - <section name="adv_opts"> - <param name="force" value="false"/> - <param name="test" value="true"/> - </section> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="true"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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_ProteinQuantifier_14 --> <test expect_num_outputs="3"> @@ -500,15 +573,18 @@ <param name="test" value="true"/> </section> <param name="in" value="ProteinQuantifier_input.idXML"/> - <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> + <output name="out" value="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" value="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> <param name="best_charge_and_fraction" value="false"/> <param name="greedy_group_resolution" value="false"/> <param name="ratios" value="false"/> <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="0"/> + <param name="aggregate" value="sum"/> + <param name="include_all" value="false"/> + </section> <section name="consensus"> <param name="normalize" value="false"/> <param name="fix_peptides" value="false"/> @@ -524,11 +600,89 @@ <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_ProteinQuantifier_15 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" value="ProteinQuantifier_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="iBAQ"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="median"/> + <param name="include_all" value="false"/> + </section> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </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_ProteinQuantifier_16 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_16_input.consensusXML"/> + <param name="design" value="ProteinQuantifier_16_input.tsv" ftype="tabular"/> + <output name="out" value="ProteinQuantifier_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="method" value="top"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="top"> + <param name="N" value="3"/> + <param name="aggregate" value="median"/> + <param name="include_all" value="true"/> + </section> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </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> </tests> <help><![CDATA[Compute peptide and protein abundances -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinQuantifier.html]]></help> <expand macro="references"/> </tool>