Mercurial > repos > iuc > freyja_boot
diff freyja_boot.xml @ 4:cd5d77d118f2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
| author | iuc |
|---|---|
| date | Wed, 19 Feb 2025 11:08:52 +0000 |
| parents | a09398bc953a |
| children |
line wrap: on
line diff
--- a/freyja_boot.xml Fri Nov 15 16:44:31 2024 +0000 +++ b/freyja_boot.xml Wed Feb 19 11:08:52 2025 +0000 @@ -12,6 +12,7 @@ <command detect_errors="exit_code"><![CDATA[ @RUN_FREYJA_UPDATE_COMMAND@ @PREPROCESS_VCF_INPUT@ +@CUSTOM_BARCODES_LINKING@ freyja boot @STANDARD_INPUT_FOR_BOOT@ --nt \${GALAXY_SLOTS:-4} @@ -101,7 +102,40 @@ </assert_contents> </output> </test> - </tests> + + <!-- Test 03: Test Custom Usher Barcode file --> + <test expect_num_outputs="4"> + <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> + <param name="variants_file" value="variants.tsv"/> + <param name="depth_file" value="depths.tsv"/> + <param name="confirmedonly" value="false"/> + <param name="nb" value="10"/> + <param name="boxplot_pdf" value="true"/> + <output name="boot_lineages" ftype="csv"> + <assert_contents> + <has_text text="B.1.617.2"/> + </assert_contents> + </output> + <output name="boot_summarized" ftype="csv"> + <assert_contents> + <has_text text="Del"/> + </assert_contents> + </output> + <output name="boot_lineages_plot" ftype="pdf"> + <assert_contents> + <has_text text="Matplot"/> + </assert_contents> + </output> + <output name="boot_summarized_plot" ftype="pdf"> + <assert_contents> + <has_text text="Matplot"/> + </assert_contents> + </output> + </test> +</tests> <help><![CDATA[ @HELP_HEADER@