| Previous changeset 3:c5f2ce99da69 (2024-11-15) Next changeset 5:e9f497a660d6 (2025-07-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06 |
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modified:
freyja_demix.xml macros.xml |
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| diff -r c5f2ce99da69 -r e7a2086a0f03 freyja_demix.xml --- a/freyja_demix.xml Fri Nov 15 16:44:54 2024 +0000 +++ b/freyja_demix.xml Wed Feb 19 11:08:36 2025 +0000 |
| [ |
| @@ -18,6 +18,7 @@ #else: #set $sn = str($sample_name.name) #end if +@CUSTOM_BARCODES_LINKING@ #set $in_file = $sn.replace(' ', '_') + '.' + $variants_in.ext ln -s '$variants_in' $in_file && freyja demix @@ -98,6 +99,24 @@ </assert_contents> </output> </test> + <!-- Test 03: Custom Usher Barcode sample --> + <test expect_num_outputs="1"> + <param name="variants_in" value="variants.tsv"/> + <param name="depth_file" value="depths.tsv"/> + <conditional name="usher_update_option"> + <param name="choice" value="custom"/> + <param name="usher_barcodes" location="https://zenodo.org/records/14888005/files/usher_barcodes.csv"/> + </conditional> + <conditional name="sample_name"> + <param name="source" value="auto"/> + </conditional> + <output name="abundances"> + <assert_contents> + <has_n_columns n="2"/> + <has_text text="AY.48"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ @HELP_HEADER@ |
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| diff -r c5f2ce99da69 -r e7a2086a0f03 macros.xml --- a/macros.xml Fri Nov 15 16:44:54 2024 +0000 +++ b/macros.xml Wed Feb 19 11:08:36 2025 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.5.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> <xrefs> @@ -22,6 +22,16 @@ freyja update && #end if ]]></token> + <token name="@CUSTOM_BARCODES_LINKING@"><![CDATA[ +#if $usher_update_option.choice == 'custom' + ln -s '${usher_update_option.usher_barcodes}' usher_barcodes.csv && +#end if + ]]></token> + <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[ +#if $usher_update_option.choice == 'custom' + --barcodes usher_barcodes.csv +#end if +]]></token> <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[ ln -s '$variants_file' 'variants_file.vcf' && ]]></token> @@ -41,11 +51,6 @@ $confirmedonly --pathogen '$pathogen' ]]></token> - <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[ -#if $usher_update_option.choice == 'custom' - --barcodes '${usher_update_option.usher_barcodes}' -#end if -]]></token> <token name="@DASH_COMMAND@"><![CDATA[ echo '${plot_format.plot_title}' > plot_title.txt && echo '${plot_format.plot_intro}' > plot_intro.txt && |