| Previous changeset 0:dda5772507b2 (2022-07-28) Next changeset 2:95e88f407e86 (2024-10-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5 |
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modified:
freyja_boot.xml macros.xml |
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| diff -r dda5772507b2 -r a09398bc953a freyja_boot.xml --- a/freyja_boot.xml Thu Jul 28 09:25:33 2022 +0000 +++ b/freyja_boot.xml Fri Jul 07 05:50:56 2023 +0000 |
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| @@ -65,20 +65,21 @@ </output> <output name="boot_summarized" ftype="csv"> <assert_contents> - <has_text text="Delta"/> + <has_text text="Del"/> </assert_contents> </output> <output name="boot_lineages_plot" ftype="pdf"> <assert_contents> - <has_text text="Matplotlib"/> + <has_text text="Matplot"/> </assert_contents> </output> <output name="boot_summarized_plot" ftype="pdf"> <assert_contents> - <has_text text="Matplotlib"/> + <has_text text="Matplot"/> </assert_contents> </output> </test> + <!-- Test 02: test VCF input file --> <test expect_num_outputs="2"> <conditional name="usher_update_option"> |
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| diff -r dda5772507b2 -r a09398bc953a macros.xml --- a/macros.xml Thu Jul 28 09:25:33 2022 +0000 +++ b/macros.xml Fri Jul 07 05:50:56 2023 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.3.8</token> + <token name="@TOOL_VERSION@">1.4.4</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> @@ -49,6 +49,7 @@ echo '${plot_format.plot_title}' > plot_title.txt && echo '${plot_format.plot_intro}' > plot_intro.txt && freyja dash + --mincov $plot_format.mincov #if $need_aggregation.choice == 'no' '$tsv_aggregated' #else @@ -61,6 +62,8 @@ ]]></token> <token name="@PLOT_COMMAND@"><![CDATA[ freyja plot + $plot_format.lineages + --mincov $plot_format.mincov #if $need_aggregation.choice == 'no' '$tsv_aggregated' #else @@ -82,6 +85,8 @@ @DASH_COMMAND@ #else if $plot_format.choice == 'plot' freyja plot + $plot_format.lineages + --mincov $plot_format.mincov #if $need_aggregation.choice == 'no' $tsv_aggregated #else @@ -129,6 +134,19 @@ checked="false" label="Remove unconfirmed lineages from the analysis" help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/> + <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue="" + checked="false" + label="Use larger library with non-public lineages" + help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/> + </xml> + <xml name="plot_lineages"> + <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue="" + checked="false" label="Use lineage specific breakdown"/> + </xml> + <xml name="plot_mincov"> + <param argument="--mincov" type="float" min="0" max="100" value="60" + label="Minimum genome coverage" + help="Include in the plot only samples where the 'coverage' value is greater than the specified --mincov parameter. It excludes samples with coverage values below the minimum coverage threshold. By default, the minimum genome coverage is set at 60 percent."/> </xml> <token name="@HELP_HEADER@"><![CDATA[ What it does @@ -145,7 +163,7 @@ ]]></token> <xml name="citations"> <citations> - <citation type="doi">10.5281/zenodo.6585067</citation> + <citation type="doi">10.1038/s41586-022-05049-6</citation> </citations> </xml> </macros> |