Add Qualifilter Galaxy wrapper #7507
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bgruening
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Dec 3, 2025
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Cool @buhlentozini. Very good quality, just some nitpicks :)
tools/qualifilter/qualifilter.xml
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| <option value="Unclassified_reads">Unclassified reads</option> | ||
| </param> | ||
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| <param name="total_reads" type="float" value="1000000" label="Minimum total reads" /> |
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can we add min/max to those parameters to help guide users?
| <param name="contam_max" type="float" value="5" label="Maximum contamination %" /> | ||
| <param name="round" type="integer" value="2" label="Rounding precision" /> | ||
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| <param name="config" type="data" format="yaml" optional="true" |
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this file should be described somewhere in more detail I think
SaimMomin12
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Dec 3, 2025
tools/qualifilter/qualifilter.xml
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| @@ -0,0 +1,143 @@ | |||
| <tool id="qualifilter" name="QualiFilter" version="@TOOL_VERSION@@VERSION_SUFFIX@" profile="21.05"> | |||
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Suggested change
| <tool id="qualifilter" name="QualiFilter" version="@TOOL_VERSION@@VERSION_SUFFIX@" profile="21.05"> | |
| <tool id="qualifilter" name="QualiFilter" version="@TOOL_VERSION@@VERSION_SUFFIX@" profile="@PROFILE@"> |
@Profile@ Token could also be introduced in the macros.xml. You can assign profile 25.0 is you like.
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com>
Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com>
SaimMomin12
reviewed
Dec 4, 2025
tools/qualifilter/qualifilter.xml
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| <param name="round" value="2" /> | ||
| <param name="derive_reads" value="true" /> | ||
| <output name="qc_matrix_tsv" file="QC_matrix.tsv"/> | ||
| <output name="qc_matrix_csv" file="QC_matrix.csv"/> |
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The log output is missing in the test. Hence the tests are failing
SaimMomin12
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Dec 11, 2025
bgruening
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Dec 12, 2025
Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
bgruening
reviewed
Dec 12, 2025
bgruening
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Dec 12, 2025
SaimMomin12
reviewed
Dec 15, 2025
SaimMomin12
approved these changes
Dec 15, 2025
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|
Thanks @buhlentozini for your contribution! |
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Deployment status: success https://github.com/galaxyproject/tools-iuc/actions/runs/20234628544 |
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Title: Add Qualifilter (QC Matrix Extractor, Bioconda-packaged)
Description:
This PR adds Qualifilter, a tool for parsing MultiQC tabular output and generating a summarized QC matrix with key sequencing and mapping metrics such as total reads, coverage, GC content, and contamination. The tool evaluates user-defined QC thresholds and reports Pass/Fail status for each sample.
Key features:
Testing:
The tool has passed Planemo lint and Planemo test locally.
Notes:
This PR supersedes #7456
, which was closed because the tool was renamed and moved to a separate repository: Qualifilter GitHub repo
.