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Fixes various tool tests #839

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Fixes various tool tests #839

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a8fdfdd
Point tool test parameters at the inputs their tools actually declare
guerler Sep 16, 2026
6d80b5f
Select the conditional branches and output counts the tool tests actu…
guerler Sep 16, 2026
7c0320f
Update the expected values the corrected test parameters now produce
guerler Sep 16, 2026
38add82
Regenerate the merged output for the corrected template parameter
guerler Sep 16, 2026
5f20e8a
Bump tool versions for the changed repositories
guerler Sep 16, 2026
5388afe
Nest test parameters in their conditionals and raise the profile wher…
guerler Sep 16, 2026
3e1337b
Replace documentation links whose hosts no longer resolve
guerler Sep 17, 2026
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2 changes: 1 addition & 1 deletion tools/bumbershoot/idpQonvertEmbedder.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="idpqonvertEmbedder" name="idpEmbedder" version="@VERSION@.1">
<tool id="idpqonvertEmbedder" name="idpEmbedder" version="@VERSION@.2">
<description>Embed human/mouse gene metadata into IDPicker files</description>
<macros>
<import>macros.xml</import>
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26 changes: 13 additions & 13 deletions tools/bumbershoot/idpassemble.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="idpassemble" name="idpAssemble" version="@VERSION@.0" profile="19.01">
<tool id="idpassemble" name="idpAssemble" version="@VERSION@.1" profile="19.01">
<description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -91,9 +91,9 @@
<test>
<param name="input" value="201208-378803-mm.idpDB" />
<param name="MaxFDRScore" value="0.05" />
<param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition.MinSpectra" value="2" />
<param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
<param name="filter_at_gene_level_condition|MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition|MinSpectra" value="2" />
<param name="filter_at_gene_level_condition|MinAdditionalPeptides" value="1" />
<param name="MinSpectraPerDistinctMatch" value="1" />
<param name="MinSpectraPerDistinctPeptide" value="1" />
<param name="MaxProteinGroupsPerPeptide" value="10" />
Expand All @@ -102,9 +102,9 @@
<test>
<param name="input" value="201208-378803-msgf.idpDB" />
<param name="MaxFDRScore" value="0.05" />
<param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition.MinSpectra" value="2" />
<param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
<param name="filter_at_gene_level_condition|MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition|MinSpectra" value="2" />
<param name="filter_at_gene_level_condition|MinAdditionalPeptides" value="1" />
<param name="MinSpectraPerDistinctMatch" value="1" />
<param name="MinSpectraPerDistinctPeptide" value="1" />
<param name="MaxProteinGroupsPerPeptide" value="10" />
Expand All @@ -113,9 +113,9 @@
<test>
<param name="input" value="201208-378803-cm.idpDB" />
<param name="MaxFDRScore" value="0.05" />
<param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition.MinSpectra" value="2" />
<param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
<param name="filter_at_gene_level_condition|MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition|MinSpectra" value="2" />
<param name="filter_at_gene_level_condition|MinAdditionalPeptides" value="1" />
<param name="MinSpectraPerDistinctMatch" value="1" />
<param name="MinSpectraPerDistinctPeptide" value="1" />
<param name="MaxProteinGroupsPerPeptide" value="10" />
Expand All @@ -126,9 +126,9 @@
<test>
<param name="input" value="201208-378803-mm.idpDB,201208-378803-msgf.idpDB,201208-378803-cm.idpDB" />
<param name="MaxFDRScore" value="0.05" />
<param name="filter_at_gene_level_condition.MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition.MinSpectra" value="2" />
<param name="filter_at_gene_level_condition.MinAdditionalPeptides" value="1" />
<param name="filter_at_gene_level_condition|MinDistinctPeptides" value="2" />
<param name="filter_at_gene_level_condition|MinSpectra" value="2" />
<param name="filter_at_gene_level_condition|MinAdditionalPeptides" value="1" />
<param name="MinSpectraPerDistinctMatch" value="1" />
<param name="MinSpectraPerDistinctPeptide" value="1" />
<param name="MaxProteinGroupsPerPeptide" value="10" />
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2 changes: 1 addition & 1 deletion tools/bumbershoot/idpqonvert.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="idpqonvert" name="idpQonvert" version="@VERSION@.0">
<tool id="idpqonvert" name="idpQonvert" version="@VERSION@.1">

@bgruening bgruening Sep 16, 2026

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@guerler can you please add profiles to all tools when we touch them? And maybe also make sure its a recent profile version?

<description>Prepare identification results for IDPicker</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/bumbershoot/idpquery.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="idpquery" name="idpQuery" version="@VERSION@.0">
<tool id="idpquery" name="idpQuery" version="@VERSION@.1">
<description>Creates text reports from idpDB files.</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/bumbershoot/myrimatch.xml
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@@ -1,4 +1,4 @@
<tool id="myrimatch" version="@VERSION@.0" name="MyriMatch">
<tool id="myrimatch" version="@VERSION@.1" name="MyriMatch">
<description>Identify peptides in tandem mass spectra.</description>
<macros>
<import>macros.xml</import>
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14 changes: 8 additions & 6 deletions tools/cardinal/classification.xml
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@@ -1,4 +1,4 @@
<tool id="cardinal_classification" name="MSI classification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<tool id="cardinal_classification" name="MSI classification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
<description>spatial classification of mass spectrometry imaging data</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -1327,7 +1327,7 @@ if (npeaks > 0 && NAcount==0){
<param name="opls_method" value="opls_analysis"/>
<param name="opls_comp" value="3"/>
<param name="opls_scale" value="FALSE"/>
<param name="PLS_Yweights" value="FALSE"/>
<param name="OPLS_Yweights" value="FALSE"/>
</conditional>
</conditional>
</conditional>
Expand Down Expand Up @@ -1365,11 +1365,11 @@ if (npeaks > 0 && NAcount==0){
<param name="class_method" value="spatialShrunkenCentroids"/>
<conditional name="ssc_analysis_cond">
<param name="ssc_method" value="ssc_cvapply"/>
<param name="ssc_r" value="1:2"/>
<param name="ssc_s" value="2:3"/>
<param name="ssc_kernel_method" value="adaptive"/>
<param name="write_best_params" value="TRUE"/>
</conditional>
<param name="ssc_r" value="1:2"/>
<param name="ssc_s" value="2:3"/>
<param name="ssc_kernel_method" value="adaptive"/>
</conditional>
</conditional>
<output name="classification_images" file="test5.pdf" compare="sim_size"/>
Expand Down Expand Up @@ -1409,7 +1409,9 @@ if (npeaks > 0 && NAcount==0){
<param name="type_method" value="prediction"/>
<param name="type_method" value="prediction"/>
<param name="training_result" value="test2.rdata" ftype="rdata"/>
<param name="classification_type" value="PLS_classifier"/>
<conditional name="classification_type_cond">
<param name="classification_type" value="PLS_classifier"/>
</conditional>
<conditional name="new_y_values_cond">
<param name="new_y_values" value="new_response"/>
<param name="new_response_file" value="pixel_annotation_file1.tabular" ftype="tabular"/>
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2 changes: 1 addition & 1 deletion tools/cardinal/group_comparison.xml
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@@ -1,4 +1,4 @@
<tool id="cardinal_group_comparison" name="MSI group comparison" version="3.8.0">
<tool id="cardinal_group_comparison" name="MSI group comparison" version="3.8.0+galaxy1">
<description>performs two group comparisons of mass spectrometry imaging data</description>
<macros>
<import>macros.xml</import>
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4 changes: 2 additions & 2 deletions tools/cardinal/macros.xml
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@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">3.4.3</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>

<xml name="requirements">
<requirements>
Expand Down Expand Up @@ -188,7 +188,7 @@ echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanil

- MSI data: 3 types of input data can be used:

- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_
- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://github.com/imzML/imzML>`_
- Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
- Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
]]></token>
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6 changes: 4 additions & 2 deletions tools/cardinal/preprocessing.xml
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@@ -1,4 +1,4 @@
<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
<description>
mass spectrometry imaging preprocessing
</description>
Expand Down Expand Up @@ -935,7 +935,9 @@ if (ncol(msidata)>0 & nrow(msidata) >0){
<repeat name="methods">
<conditional name="methods_conditional">
<param name="preprocessing_method" value="Normalization"/>
<param name="normalization_method" value="tic"/>
<conditional name="methods_for_normalization">
<param name="normalization_method" value="tic"/>
</conditional>
</conditional>
</repeat>
<repeat name="methods">
Expand Down
27 changes: 0 additions & 27 deletions tools/cardinal/segmentation.xml
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Expand Up @@ -396,15 +396,6 @@ if (npeaks > 0 && NAcount==0)
<param name="kmeans_r" value="1:3"/>
<param name="kmeans_k" value="2,3"/>
<param name="kmeans_toplabels" value="20"/>
<repeat name="colours">
<param name="feature_color" value="#ff00ff"/>
</repeat>
<repeat name="colours">
<param name="feature_color" value="#0000FF"/>
</repeat>
<repeat name="colours">
<param name="feature_color" value="#00C957"/>
</repeat>
<param name="output_rdata" value="True"/>
<output name="segmentationimages" file="kmeans_analyze.pdf" compare="sim_size"/>
<output name="mzfeatures" file="toplabels_skm.tabular"/>
Expand All @@ -417,15 +408,6 @@ if (npeaks > 0 && NAcount==0)
<param name="centroids_r" value="1,2"/>
<param name="centroids_k" value="3"/>
<param name="centroids_toplabels" value="50"/>
<repeat name="colours">
<param name="feature_color" value="#0000FF"/>
</repeat>
<repeat name="colours">
<param name="feature_color" value="#00C957"/>
</repeat>
<repeat name="colours">
<param name="feature_color" value="#B0171F"/>
</repeat>
<output name="segmentationimages" file="centroids_rdata.pdf" compare="sim_size"/>
<output name="mzfeatures" file="toplabels_ssc.tabular"/>
<output name="pixeloutput" file="classes_ssc.tabular"/>
Expand All @@ -442,15 +424,6 @@ if (npeaks > 0 && NAcount==0)
<param name="centroids_k" value="2,3"/>
<param name="centroids_s" value="0,3"/>
<param name="centroids_toplabels" value="100"/>
<repeat name="colours">
<param name="feature_color" value="#0000FF"/>
</repeat>
<repeat name="colours">
<param name="feature_color" value="#00C957"/>
</repeat>
<repeat name="colours">
<param name="feature_color" value="#B0171F"/>
</repeat>
<output name="segmentationimages" ftype="pdf">
<assert_contents>
<has_size value="1206464" delta="100"/>
Expand Down
22 changes: 12 additions & 10 deletions tools/cardinal/spectra_plots.xml
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Expand Up @@ -621,16 +621,18 @@ print(position_df)
<conditional name="single_or_overlaid">
<param name="plot_type" value="overlaid_plots"/>
<param name="column_pixel_annotation" value="4"/>
<param name="colour_type" value="manual_colour"/>
<repeat name="colours">
<param name="annotation_color" value="#0000FF"/>
</repeat>
<repeat name="colours">
<param name="annotation_color" value="#00C957"/>
</repeat>
<repeat name="colours">
<param name="annotation_color" value="#B0171F"/>
</repeat>
<conditional name="colour_conditional">
<param name="colour_type" value="manual_colour"/>
<repeat name="colours">
<param name="annotation_color" value="#0000FF"/>
</repeat>
<repeat name="colours">
<param name="annotation_color" value="#00C957"/>
</repeat>
<repeat name="colours">
<param name="annotation_color" value="#B0171F"/>
</repeat>
</conditional>
</conditional>
</conditional>
<param name="fullmz" value="FALSE"/>
Expand Down
2 changes: 1 addition & 1 deletion tools/cardinal/test-data/best_r_test5.txt
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@@ -1 +1 @@
2
1
4 changes: 2 additions & 2 deletions tools/maxquant/macros.xml
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Expand Up @@ -2,8 +2,8 @@
<macros>
<token name="@PROFILE@">21.05</token>
<token name="@VERSION@">2.0.3.0</token>
<token name="@VERSION_SUFFIX@">3</token>
<token name="@VERSION_SUFFIX_MQPAR@">3</token>
<token name="@VERSION_SUFFIX@">4</token>
<token name="@VERSION_SUFFIX_MQPAR@">4</token>
<token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
<token name="@TMT2PLEX@">
- [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
Expand Down
2 changes: 1 addition & 1 deletion tools/maxquant/maxquant.xml
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Expand Up @@ -986,7 +986,7 @@ short peptides are usually not unique in the protein database and therefore not
<output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" />
</test>
<!-- 9 TMTpro18plex test -->
<test expect_num_outputs="2">
<test expect_num_outputs="1">
<section name="input_opts">
<param name="fasta_files" value="tmt_data_18.fasta" />
<param name="identifier_parse_rule" value="&gt;([^\s]*)" />
Expand Down
3 changes: 1 addition & 2 deletions tools/moFF/moff.xml
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@@ -1,4 +1,4 @@
<tool id="proteomics_moff" name="moFF" version="@VERSION@.0">
<tool id="proteomics_moff" name="moFF" version="@VERSION@.1">
<description>extracts MS1 intensities from spectrum files</description>
<macros>
<token name="@VERSION@">2.0.3</token>
Expand Down Expand Up @@ -327,7 +327,6 @@
<element name="mbr_test2" value="input/mbr_test2.tabular"/>
</collection>
</param>
<param name="ext" value="tabular"/>
<output_collection name="ident_output_mbr" type="list" count="2">
<element name="mbr_test1_match">
<assert_contents>
Expand Down
4 changes: 2 additions & 2 deletions tools/morpheus/macros.xml
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@@ -1,7 +1,7 @@
<macros>
<token name="@TOOL_VERSION@">288</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">22.05</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">24.2</token>
<xml name="edam_ontology">
<edam_topics>
<edam_topic>topic_0121</edam_topic>
Expand Down
20 changes: 10 additions & 10 deletions tools/morpheus/morpheus.xml
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Expand Up @@ -211,7 +211,6 @@
<param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
<param name="fdr" value="1"/>
<param name="mvmi" value="1024"/>
<param name="precmt" value="Monoisotopic"/>
<param name="precmtu" value="Da"/>
<param name="precmtv" value="2.5"/>
<output name="output_psms">
Expand All @@ -227,7 +226,6 @@
<param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
<param name="fdr" value="1"/>
<param name="mvmi" value="1024"/>
<param name="precmt" value="Monoisotopic"/>
<param name="precmtu" value="Da"/>
<param name="precmtv" value="2.5"/>
<param name="fm" value="carbamidomethylation of C"/>
Expand All @@ -244,7 +242,6 @@
<param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
<param name="fdr" value="1"/>
<param name="mvmi" value="1024"/>
<param name="precmt" value="Monoisotopic"/>
<param name="precmtu" value="Da"/>
<param name="precmtv" value="2.5"/>
<param name="fm" value="carbamidomethylation of C"/>
Expand All @@ -262,7 +259,6 @@
<param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
<param name="fdr" value="1"/>
<param name="mvmi" value="1024"/>
<param name="precmt" value="Monoisotopic"/>
<param name="precmtu" value="Da"/>
<param name="precmtv" value="2.5"/>
<param name="fm" value="carbamidomethylation of C"/>
Expand All @@ -279,13 +275,15 @@
<param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
<param name="fdr" value="1"/>
<param name="mvmi" value="1024"/>
<param name="precmt" value="Monoisotopic"/>
<param name="precmtu" value="Da"/>
<param name="precmtv" value="2.5"/>
<param name="fm" value="carbamidomethylation of C"/>
<param name="vm" value="oxidation of M"/>
<param name="adv_options_selector" value="set"/>
<param name="prodmtv" value=".01"/>
<conditional name="advanced">
<param name="adv_options_selector" value="set"/>
<param name="precmt" value="Monoisotopic"/>
<param name="prodmtv" value=".01"/>
</conditional>
<output name="output_psms">
<assert_contents>
<has_text text="K.KTLKSDGVAGLYR.G" />
Expand All @@ -298,14 +296,16 @@
<param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
<param name="fdr" value="1"/>
<param name="mvmi" value="1024"/>
<param name="precmt" value="Monoisotopic"/>
<param name="precmtu" value="Da"/>
<param name="precmtv" value="2.5"/>
<param name="fm" value="carbamidomethylation of C"/>
<param name="vm" value="oxidation of M"/>
<param name="p" value="trypsin"/>
<param name="adv_options_selector" value="set"/>
<param name="prodmtv" value=".01"/>
<conditional name="advanced">
<param name="adv_options_selector" value="set"/>
<param name="precmt" value="Monoisotopic"/>
<param name="prodmtv" value=".01"/>
</conditional>
<output name="output_psms">
<assert_contents>
<has_text text="K.KTLKSDGVAGLYR.G" />
Expand Down
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