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updated recetox-aplcms to 0.14.0 and added raw file reading capacity #700

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updated recetox-aplcms to 0.14.0 and added raw file reading capacity #700

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881f5b0
updated tools and initial version
hechth Jul 25, 2025
26dcd07
added dependencies and configfiles to install rawrr - currently waiti…
hechth Aug 13, 2025
5c3b4d2
Fixed raw file reasing in the test and updated to 0.14.1
hechth Aug 15, 2025
8cadee5
using soft symlink or copying in case of raw file, currently there is…
hechth Aug 15, 2025
90f4834
trying tests with remote files urls
hechth Oct 17, 2025
e3d3b74
Merge branch 'master' into hechth/issue694
hechth Dec 12, 2025
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5 changes: 3 additions & 2 deletions tools/recetox_aplcms/macros.xml
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@@ -1,9 +1,10 @@
<macros>
<token name="@TOOL_VERSION@">0.13.4</token>
<token name="@TOOL_VERSION@">0.14.1</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
<requirement type="package" version="2.5.2">pymzml</requirement>
<requirement type="package" version="2.5.11">pymzml</requirement>
<yield />
</requirements>
</xml>

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15 changes: 13 additions & 2 deletions tools/recetox_aplcms/recetox_aplcms_align_features.xml
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<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_align_features" name="recetox-aplcms - align features" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>align peaks across samples</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -56,7 +56,18 @@
</outputs>

<tests>
<test expect_failure="true" />
<test expect_num_outputs="3">
<param name="files" ftype="parquet">
<collection type="list">
<element name="RCX_06_shortened_extracted_clusters.parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/clusters/RCX_06_shortened_extracted_clusters.parquet?ref_type=heads&amp;inline=false"/>
<element name="RCX_07_shortened_extracted_clusters.parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/clusters/RCX_07_shortened_extracted_clusters.parquet?ref_type=heads&amp;inline=false"/>
<element name="RCX_08_shortened_extracted_clusters.parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/clusters/RCX_08_shortened_extracted_clusters.parquet?ref_type=heads&amp;inline=false"/>
</collection>
</param>
<output name="metadata_file" ftype="parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/aligned/metadata_table.parquet?ref_type=heads&amp;inline=false"/>
<output name="rt_file" ftype="parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/aligned/rt_table.parquet?ref_type=heads&amp;inline=false"/>
<output name="intensity_file" ftype="parquet" location="https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/aligned/intensity_table.parquet?ref_type=heads&amp;inline=false"/>
</test>
</tests>

<help>
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2 changes: 1 addition & 1 deletion tools/recetox_aplcms/recetox_aplcms_compute_clusters.xml
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@@ -1,4 +1,4 @@
<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_compute_clusters" name="recetox-aplcms - compute clusters" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>compute clusters of mz and rt across samples and assign cluster IDs to individual features</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/recetox_aplcms/recetox_aplcms_compute_template.xml
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<tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>compute retention time correction template feature table</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/recetox_aplcms/recetox_aplcms_correct_time.xml
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<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>correct retention time across samples for peak alignment</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/recetox_aplcms/recetox_aplcms_generate_feature_table.xml
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<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>generate feature table from noise-removed HRMS profile data</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/recetox_aplcms/recetox_aplcms_merge_known_table.xml
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<tool id="recetox_aplcms_merge_known_table" name="recetox-aplcms - merge known table" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_merge_known_table" name="recetox-aplcms - merge known table" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>join knowledge from aligned features and known table.</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/recetox_aplcms/recetox_aplcms_recover_weaker_signals.xml
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@@ -1,4 +1,4 @@
<tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>recover weaker signals from raw data using an aligned feature table</description>
<macros>
<import>macros.xml</import>
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39 changes: 33 additions & 6 deletions tools/recetox_aplcms/recetox_aplcms_remove_noise.xml
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<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="21.09">
<tool id="recetox_aplcms_remove_noise" name="recetox-aplcms - remove noise" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<description>filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data</description>
<macros>
<import>macros.xml</import>
Expand All @@ -10,18 +10,29 @@
</edam_operations>
<expand macro="refs"/>
<expand macro="creator"/>
<expand macro="requirements"/>
<expand macro="requirements">
<requirement type="package" version="1.10.2">bioconductor-rawrr</requirement>
<!-- <requirement type="package" version="6.12.0.199">mono</requirement> -->
</expand>

<command detect_errors="aggressive"><![CDATA[
python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
#if $input_file.ext == 'thermo.raw':
cp $input_file input.$input_file.ext &&
Rscript -e 'source("${install_rawrr}")' &&
Rscript -e 'source("${raw_id_getter}")' &&
Rscript -e "future::plan(future::multicore, workers = \${GALAXY_SLOTS:-1})" &&
#else:
ln -s $input_file input.$input_file.ext &&
python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
#end if
Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' -e 'future::plan(future::sequential)'
]]></command>
<configfiles>
<configfile name="run_script"><![CDATA[
sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)

profile <- remove_noise(
filename = '$input_file',
filename = 'input.${input_file.ext}',
min_pres = $min_pres,
min_run = $min_run,
mz_tol = ${mz_tol}/1e6,
Expand All @@ -36,10 +47,21 @@
profile <- save_sample_name(profile, sample_name)
save_data_as_parquet_file(profile, '$output_file')
]]></configfile>

<configfile name="raw_id_getter"><![CDATA[
header <- rawrr::readFileHeader('input.${input_file.ext}')
writeLines(header[['Sample id']], "sample_name.txt")
]]></configfile>

<configfile name="install_rawrr"><![CDATA[
rawrr::installRawFileReaderDLLs()
rawrr::installRawrrExe()
rawrr::rawrrAssemblyPath()
]]></configfile>
</configfiles>

<inputs>
<param label="Input spectra data" name="input_file" type="data" format="mzml"
<param label="Input spectra data" name="input_file" type="data" format="mzml,thermo.raw"
help="Sample data in .mzml format acquired in profile mode." />
<expand macro="remove_noise_params"/>
</inputs>
Expand All @@ -58,6 +80,11 @@
<param name="grouping_threshold" value="2" />
<output name="output_file" file="remove_noise_docker_threshold.parquet" ftype="parquet" />
</test>
<test>
<param name="input_file" ftype="thermo.raw" location="https://zenodo.org/records/7890956/files/8_qc_no_dil_milliq.raw?download=1"/>
<param name="grouping_threshold" value="2" />
<output name="output_file" ftype="parquet" md5="a43a29b2e79c59d40bfb8c24c674f899"/>
</test>
</tests>

<help>
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