From 9421dbc43828877bf76cb61bde992ec3c25d5022 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 16 Sep 2026 14:52:04 +0300 Subject: [PATCH 1/7] Point tool test parameters at the inputs their tools actually declare --- tools/bumbershoot/idpassemble.xml | 24 ++++++++--------- tools/cardinal/classification.xml | 2 +- tools/cardinal/segmentation.xml | 27 ------------------- tools/lfq_protein_quant/lfq_protein_quant.xml | 1 - tools/moFF/moff.xml | 1 - tools/msstats/msstats.xml | 2 +- 6 files changed, 14 insertions(+), 43 deletions(-) diff --git a/tools/bumbershoot/idpassemble.xml b/tools/bumbershoot/idpassemble.xml index 33b702cc8..0bea656c3 100644 --- a/tools/bumbershoot/idpassemble.xml +++ b/tools/bumbershoot/idpassemble.xml @@ -91,9 +91,9 @@ - - - + + + @@ -102,9 +102,9 @@ - - - + + + @@ -113,9 +113,9 @@ - - - + + + @@ -126,9 +126,9 @@ - - - + + + diff --git a/tools/cardinal/classification.xml b/tools/cardinal/classification.xml index 14def9c2a..1e29ad015 100644 --- a/tools/cardinal/classification.xml +++ b/tools/cardinal/classification.xml @@ -1327,7 +1327,7 @@ if (npeaks > 0 && NAcount==0){ - + diff --git a/tools/cardinal/segmentation.xml b/tools/cardinal/segmentation.xml index b24672ac3..b20234e65 100644 --- a/tools/cardinal/segmentation.xml +++ b/tools/cardinal/segmentation.xml @@ -396,15 +396,6 @@ if (npeaks > 0 && NAcount==0) - - - - - - - - - @@ -417,15 +408,6 @@ if (npeaks > 0 && NAcount==0) - - - - - - - - - @@ -442,15 +424,6 @@ if (npeaks > 0 && NAcount==0) - - - - - - - - - diff --git a/tools/lfq_protein_quant/lfq_protein_quant.xml b/tools/lfq_protein_quant/lfq_protein_quant.xml index 9201609b1..0d4a2d590 100644 --- a/tools/lfq_protein_quant/lfq_protein_quant.xml +++ b/tools/lfq_protein_quant/lfq_protein_quant.xml @@ -39,7 +39,6 @@ - diff --git a/tools/moFF/moff.xml b/tools/moFF/moff.xml index 1f7526ce0..059c74613 100644 --- a/tools/moFF/moff.xml +++ b/tools/moFF/moff.xml @@ -327,7 +327,6 @@ - diff --git a/tools/msstats/msstats.xml b/tools/msstats/msstats.xml index 4d4d12c55..0a25bdf13 100644 --- a/tools/msstats/msstats.xml +++ b/tools/msstats/msstats.xml @@ -871,9 +871,9 @@ write.table(comparisons\$ModelQC, "ModelQC.tsv", sep = "\t", quote = F, row.name +
-
From ce0970cdbf4b4728a0590655f626718fe9adc70a Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 16 Sep 2026 16:33:21 +0300 Subject: [PATCH 2/7] Select the conditional branches and output counts the tool tests actually exercise --- tools/cardinal/classification.xml | 6 +++--- tools/cardinal/spectra_plots.xml | 22 ++++++++++++---------- tools/maxquant/maxquant.xml | 2 +- tools/morpheus/morpheus.xml | 4 ---- tools/msstats/msstats.xml | 2 ++ tools/pyprophet/pyprophet_merge.xml | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-) diff --git a/tools/cardinal/classification.xml b/tools/cardinal/classification.xml index 1e29ad015..7a649b869 100644 --- a/tools/cardinal/classification.xml +++ b/tools/cardinal/classification.xml @@ -1365,11 +1365,11 @@ if (npeaks > 0 && NAcount==0){ - - - + + + diff --git a/tools/cardinal/spectra_plots.xml b/tools/cardinal/spectra_plots.xml index 619c4a57d..ef03aed36 100644 --- a/tools/cardinal/spectra_plots.xml +++ b/tools/cardinal/spectra_plots.xml @@ -621,16 +621,18 @@ print(position_df) - - - - - - - - - - + + + + + + + + + + + + diff --git a/tools/maxquant/maxquant.xml b/tools/maxquant/maxquant.xml index 171378b7e..f9eb7e36b 100755 --- a/tools/maxquant/maxquant.xml +++ b/tools/maxquant/maxquant.xml @@ -986,7 +986,7 @@ short peptides are usually not unique in the protein database and therefore not - +
diff --git a/tools/morpheus/morpheus.xml b/tools/morpheus/morpheus.xml index d6125cd54..e5c174bb3 100644 --- a/tools/morpheus/morpheus.xml +++ b/tools/morpheus/morpheus.xml @@ -211,7 +211,6 @@ - @@ -227,7 +226,6 @@ - @@ -244,7 +242,6 @@ - @@ -262,7 +259,6 @@ - diff --git a/tools/msstats/msstats.xml b/tools/msstats/msstats.xml index 0a25bdf13..988f5e828 100644 --- a/tools/msstats/msstats.xml +++ b/tools/msstats/msstats.xml @@ -928,6 +928,8 @@ write.table(comparisons\$ModelQC, "ModelQC.tsv", sep = "\t", quote = F, row.name + + diff --git a/tools/pyprophet/pyprophet_merge.xml b/tools/pyprophet/pyprophet_merge.xml index 98f1916ba..bd3ddbfbb 100644 --- a/tools/pyprophet/pyprophet_merge.xml +++ b/tools/pyprophet/pyprophet_merge.xml @@ -28,7 +28,7 @@ - + From 195e878e55a18412081f09b4302b39472cd3d746 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 16 Sep 2026 18:34:34 +0300 Subject: [PATCH 3/7] Update the expected values the corrected test parameters now produce --- tools/cardinal/test-data/best_r_test5.txt | 2 +- tools/msstats/msstats.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/cardinal/test-data/best_r_test5.txt b/tools/cardinal/test-data/best_r_test5.txt index 0cfbf0888..d00491fd7 100644 --- a/tools/cardinal/test-data/best_r_test5.txt +++ b/tools/cardinal/test-data/best_r_test5.txt @@ -1 +1 @@ -2 +1 diff --git a/tools/msstats/msstats.xml b/tools/msstats/msstats.xml index 988f5e828..5d808d4bc 100644 --- a/tools/msstats/msstats.xml +++ b/tools/msstats/msstats.xml @@ -954,7 +954,7 @@ write.table(comparisons\$ModelQC, "ModelQC.tsv", sep = "\t", quote = F, row.name - + From e2b256b31cbfe84a9b9d30258498768973da12d0 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 16 Sep 2026 20:58:44 +0300 Subject: [PATCH 4/7] Regenerate the merged output for the corrected template parameter --- tools/pyprophet/test-data/merged.osw | Bin 327680 -> 315392 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git 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z%wY9f5x8__U-P7EeJ}!47NjBP;!MLz>+(Nk3{-MBz;jgfjlkdCYY6aSSC*za!M5fp zE8*&df({4FnY!+FRC)J&0z9emL<62wx$g-szfCb3NoNP(pX0&vIO_P`!a#~KP+xzz zvHk9>wWS%9NMfH`IWMM|LFm#iJz%b)Lw26Phew0<*|K4?=`|Ds1s!^^h_JSTy2A`z z5%*EXKt+euOt($?byl2X76DowYm}wz#m}>?-B;5L)OFZQb^uV6ubhS^Tqcs8jkHy4Svo7?^gl8Niae}f z;pD>;CdVIIiGxRCO@iX+z=|E!qi6<7JxmboKB4<8h*7wLE}HZ1Ul!2NL?*LnDYK!BJ zz Date: Wed, 16 Sep 2026 21:13:28 +0300 Subject: [PATCH 5/7] Bump tool versions for the changed repositories --- tools/bumbershoot/idpQonvertEmbedder.xml | 2 +- tools/bumbershoot/idpassemble.xml | 2 +- tools/bumbershoot/idpqonvert.xml | 2 +- tools/bumbershoot/idpquery.xml | 2 +- tools/bumbershoot/myrimatch.xml | 2 +- tools/cardinal/group_comparison.xml | 2 +- tools/cardinal/macros.xml | 2 +- tools/lfq_protein_quant/lfq_protein_quant.xml | 1 + tools/maxquant/macros.xml | 4 ++-- tools/moFF/moff.xml | 2 +- tools/morpheus/macros.xml | 2 +- tools/msstats/msstats.xml | 2 +- tools/pyprophet/pyprophet_export.xml | 2 +- tools/pyprophet/pyprophet_merge.xml | 2 +- tools/pyprophet/pyprophet_peptide.xml | 2 +- tools/pyprophet/pyprophet_protein.xml | 2 +- tools/pyprophet/pyprophet_score.xml | 2 +- tools/pyprophet/pyprophet_subsample.xml | 2 +- 18 files changed, 19 insertions(+), 18 deletions(-) diff --git a/tools/bumbershoot/idpQonvertEmbedder.xml b/tools/bumbershoot/idpQonvertEmbedder.xml index a0eb2aabc..7325e8892 100644 --- a/tools/bumbershoot/idpQonvertEmbedder.xml +++ b/tools/bumbershoot/idpQonvertEmbedder.xml @@ -1,5 +1,5 @@ - + Embed human/mouse gene metadata into IDPicker files macros.xml diff --git a/tools/bumbershoot/idpassemble.xml b/tools/bumbershoot/idpassemble.xml index 0bea656c3..c230fe7f6 100644 --- a/tools/bumbershoot/idpassemble.xml +++ b/tools/bumbershoot/idpassemble.xml @@ -1,5 +1,5 @@ - + Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels. macros.xml diff --git a/tools/bumbershoot/idpqonvert.xml b/tools/bumbershoot/idpqonvert.xml index 0589f59f1..2273f17e2 100644 --- a/tools/bumbershoot/idpqonvert.xml +++ b/tools/bumbershoot/idpqonvert.xml @@ -1,5 +1,5 @@ - + Prepare identification results for IDPicker macros.xml diff --git a/tools/bumbershoot/idpquery.xml b/tools/bumbershoot/idpquery.xml index b5c2cf811..72c85c0ea 100644 --- a/tools/bumbershoot/idpquery.xml +++ b/tools/bumbershoot/idpquery.xml @@ -1,5 +1,5 @@ - + Creates text reports from idpDB files. macros.xml diff --git a/tools/bumbershoot/myrimatch.xml b/tools/bumbershoot/myrimatch.xml index c743f0100..e78e97c4e 100644 --- a/tools/bumbershoot/myrimatch.xml +++ b/tools/bumbershoot/myrimatch.xml @@ -1,4 +1,4 @@ - + Identify peptides in tandem mass spectra. macros.xml diff --git a/tools/cardinal/group_comparison.xml b/tools/cardinal/group_comparison.xml index f090c1cf4..778a8cc5b 100644 --- a/tools/cardinal/group_comparison.xml +++ b/tools/cardinal/group_comparison.xml @@ -1,4 +1,4 @@ - + performs two group comparisons of mass spectrometry imaging data macros.xml diff --git a/tools/cardinal/macros.xml b/tools/cardinal/macros.xml index 968506d9c..526e1ec95 100644 --- a/tools/cardinal/macros.xml +++ b/tools/cardinal/macros.xml @@ -1,6 +1,6 @@ 3.4.3 - 0 + 1 diff --git a/tools/lfq_protein_quant/lfq_protein_quant.xml b/tools/lfq_protein_quant/lfq_protein_quant.xml index 0d4a2d590..9201609b1 100644 --- a/tools/lfq_protein_quant/lfq_protein_quant.xml +++ b/tools/lfq_protein_quant/lfq_protein_quant.xml @@ -39,6 +39,7 @@ + diff --git a/tools/maxquant/macros.xml b/tools/maxquant/macros.xml index d1db9aaa5..f0e03a072 100644 --- a/tools/maxquant/macros.xml +++ b/tools/maxquant/macros.xml @@ -2,8 +2,8 @@ 21.05 2.0.3.0 - 3 - 3 + 4 + 4 [^\w\-\s\.] - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] diff --git a/tools/moFF/moff.xml b/tools/moFF/moff.xml index 059c74613..acc95d2d1 100644 --- a/tools/moFF/moff.xml +++ b/tools/moFF/moff.xml @@ -1,4 +1,4 @@ - + extracts MS1 intensities from spectrum files 2.0.3 diff --git a/tools/morpheus/macros.xml b/tools/morpheus/macros.xml index c843ed1ca..cc6300270 100644 --- a/tools/morpheus/macros.xml +++ b/tools/morpheus/macros.xml @@ -1,6 +1,6 @@ 288 - 0 + 1 22.05 diff --git a/tools/msstats/msstats.xml b/tools/msstats/msstats.xml index 5d808d4bc..0d08ccc3d 100644 --- a/tools/msstats/msstats.xml +++ b/tools/msstats/msstats.xml @@ -2,7 +2,7 @@ statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry 4.0.0 - 1 + 2 diff --git a/tools/pyprophet/pyprophet_export.xml b/tools/pyprophet/pyprophet_export.xml index 434a0a218..db4ca6951 100644 --- a/tools/pyprophet/pyprophet_export.xml +++ b/tools/pyprophet/pyprophet_export.xml @@ -1,4 +1,4 @@ - + Export tabular files, optional swath2stats export diff --git a/tools/pyprophet/pyprophet_merge.xml b/tools/pyprophet/pyprophet_merge.xml index bd3ddbfbb..1b33de069 100644 --- a/tools/pyprophet/pyprophet_merge.xml +++ b/tools/pyprophet/pyprophet_merge.xml @@ -1,4 +1,4 @@ - + Merge multiple osw files diff --git a/tools/pyprophet/pyprophet_peptide.xml b/tools/pyprophet/pyprophet_peptide.xml index c36c1870f..082da5e5e 100644 --- a/tools/pyprophet/pyprophet_peptide.xml +++ b/tools/pyprophet/pyprophet_peptide.xml @@ -1,4 +1,4 @@ - + Peptide error-rate estimation diff --git a/tools/pyprophet/pyprophet_protein.xml b/tools/pyprophet/pyprophet_protein.xml index d33dfa806..0ea2f1ff3 100644 --- a/tools/pyprophet/pyprophet_protein.xml +++ b/tools/pyprophet/pyprophet_protein.xml @@ -1,4 +1,4 @@ - + Protein error-rate estimation diff --git a/tools/pyprophet/pyprophet_score.xml b/tools/pyprophet/pyprophet_score.xml index 72b41e718..3f6bd903f 100644 --- a/tools/pyprophet/pyprophet_score.xml +++ b/tools/pyprophet/pyprophet_score.xml @@ -1,4 +1,4 @@ - + Error-rate estimation for MS1, MS2 and transition-level data diff --git a/tools/pyprophet/pyprophet_subsample.xml b/tools/pyprophet/pyprophet_subsample.xml index a549748b6..a21d09eb2 100644 --- a/tools/pyprophet/pyprophet_subsample.xml +++ b/tools/pyprophet/pyprophet_subsample.xml @@ -1,4 +1,4 @@ - + Subsample OpenSWATH file From 3b842e843ef17d31c211665ee05c1b078198f5f1 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 16 Sep 2026 21:48:15 +0300 Subject: [PATCH 6/7] Nest test parameters in their conditionals and raise the profile where tests validate --- tools/cardinal/classification.xml | 6 ++++-- tools/cardinal/preprocessing.xml | 6 ++++-- tools/morpheus/macros.xml | 2 +- tools/morpheus/morpheus.xml | 16 ++++++++++------ 4 files changed, 19 insertions(+), 11 deletions(-) diff --git a/tools/cardinal/classification.xml b/tools/cardinal/classification.xml index 7a649b869..92d0c6052 100644 --- a/tools/cardinal/classification.xml +++ b/tools/cardinal/classification.xml @@ -1,4 +1,4 @@ - + spatial classification of mass spectrometry imaging data macros.xml @@ -1409,7 +1409,9 @@ if (npeaks > 0 && NAcount==0){ - + + + diff --git a/tools/cardinal/preprocessing.xml b/tools/cardinal/preprocessing.xml index bd867958f..641a2e805 100644 --- a/tools/cardinal/preprocessing.xml +++ b/tools/cardinal/preprocessing.xml @@ -1,4 +1,4 @@ - + mass spectrometry imaging preprocessing @@ -935,7 +935,9 @@ if (ncol(msidata)>0 & nrow(msidata) >0){ - + + + diff --git a/tools/morpheus/macros.xml b/tools/morpheus/macros.xml index cc6300270..42ecebd6b 100644 --- a/tools/morpheus/macros.xml +++ b/tools/morpheus/macros.xml @@ -1,7 +1,7 @@ 288 1 - 22.05 + 24.2 topic_0121 diff --git a/tools/morpheus/morpheus.xml b/tools/morpheus/morpheus.xml index e5c174bb3..8b70487b9 100644 --- a/tools/morpheus/morpheus.xml +++ b/tools/morpheus/morpheus.xml @@ -275,13 +275,15 @@ - - - + + + + + @@ -294,14 +296,16 @@ - - - + + + + + From 5a9a1cb9998a6c80f2c08c14f34c9573b7db0feb Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 17 Sep 2026 11:14:08 +0300 Subject: [PATCH 7/7] Replace documentation links whose hosts no longer resolve --- tools/cardinal/macros.xml | 2 +- tools/msstats/msstats.xml | 2 +- tools/pyprophet/macros.xml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/cardinal/macros.xml b/tools/cardinal/macros.xml index 526e1ec95..cf13836d8 100644 --- a/tools/cardinal/macros.xml +++ b/tools/cardinal/macros.xml @@ -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 `_ + - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format `_ - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData ]]> diff --git a/tools/msstats/msstats.xml b/tools/msstats/msstats.xml index 0d08ccc3d..6e62ecaf9 100644 --- a/tools/msstats/msstats.xml +++ b/tools/msstats/msstats.xml @@ -1025,7 +1025,7 @@ The MSstats Galaxy tool (version @TOOL_VERSION@) allows the detection of differe **Input data** -- Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant `_, `OpenSWATH `_ +- Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant `_, `OpenSWATH `_ - MSstats format: tabular file with 10 column either manually curated or other sources such as Swath2stats tool which is implemented in Pyprophet export in Galaxy. For manual curation: Names of headers are fixed but not case sensitive: diff --git a/tools/pyprophet/macros.xml b/tools/pyprophet/macros.xml index 6d03c7279..69ba91a85 100644 --- a/tools/pyprophet/macros.xml +++ b/tools/pyprophet/macros.xml @@ -18,6 +18,6 @@ - http://openswath.org/en/latest/docs/pyprophet.html + https://openswath.readthedocs.io/en/latest/docs/pyprophet.html