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Update Cardinal Version 3.4.3 #763

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merged 18 commits into from
Jul 4, 2024

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MarenStillger
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This PR updates Cardinal to version 3.4.3.

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@bernt-matthias bernt-matthias left a comment

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Just two technical comments from my side.

<description>spatial classification of mass spectrometry imaging data</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements">
<requirement type="package" version="2.3">r-gridextra</requirement>
<requirement type="package" version="3.3.5">r-ggplot2</requirement>
<!--requirement type="package" version="2.3">r-gridextra</requirement>
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We can just remove instead of comment. git stores it anyway.

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thanks, updated it accordingly :)

</expand>
<command detect_errors="exit_code">
<![CDATA[
#for $i, $infile in enumerate($infiles):
#if $infile.ext == 'imzml'
ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd &&
cp '${infile.extra_files_path}/imzml' infile_${i}.imzML &&
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Is copying really necessary?

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unfortunately yes, otherwise neither imzml nor analyze75 files will be loaded

@@ -1,4 +1,4 @@
<tool id="cardinal_data_exporter" name="MSI data exporter" version="@[email protected]">
<tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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please add also a profile="22.05" to each tool

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thanks, added the profile to all tools 👍

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@bgruening bgruening left a comment

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Cool, thanks a lot!

@bgruening bgruening enabled auto-merge July 4, 2024 12:33
@bgruening bgruening merged commit 91e77c1 into galaxyproteomics:master Jul 4, 2024
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3 participants