Mercurial > repos > iuc > snpfreqplot
diff snpfreqplot.xml @ 1:e362b3143cde draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"
| author | iuc |
|---|---|
| date | Thu, 10 Dec 2020 13:41:29 +0000 |
| parents | 1062d6ad6503 |
| children | dc51db22310c |
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--- a/snpfreqplot.xml Wed Dec 02 21:23:06 2020 +0000 +++ b/snpfreqplot.xml Thu Dec 10 13:41:29 2020 +0000 @@ -3,14 +3,13 @@ <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description> <macros> <token name="@VERSION@">1.0</token> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <requirements> <requirement type="package" version="4.0">r-base</requirement> <requirement type="package" version="1.0.12">r-pheatmap</requirement> <requirement type="package" version="1.3.0">r-tidyverse</requirement> <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement> - <requirement type="package" version="">xorg-libxt</requirement> </requirements> <edam_topics> <edam_topic>topic_0797</edam_topic> @@ -187,7 +186,7 @@ <param name="color" value="Spectral" /> <param name="output_type" value="png" /> </section> - <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="86000" /> + <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="100000" /> </test> <test expect_num_outputs="1"> <!-- SVG, clustering defaults --> @@ -202,7 +201,7 @@ </section> <output name="outfile" ftype="svg"> <assert_contents> - <has_text text="viewBox="0 0 1156 335"" /> + <has_text text="viewBox="0 0 1156 361"" /> </assert_contents> </output> </test> @@ -219,7 +218,7 @@ <param name="ratio" value="1.2" /> <param name="output_type" value="jpeg" /> </section> - <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="121000" /> + <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="130000" /> </test> <test expect_num_outputs="1"> <!-- PDF, vcf test --> @@ -238,7 +237,7 @@ </section> <output name="outfile" ftype="svg"> <assert_contents> - <has_text text="viewBox="0 0 754 271"" /> + <has_text text="viewBox="0 0 754 292"" /> </assert_contents> </output> </test> @@ -251,7 +250,7 @@ </section> <output name="outfile" ftype="svg"> <assert_contents> - <has_text text="viewBox="0 0 3101 697"" /> + <has_text text="viewBox="0 0 3101 879"" /> </assert_contents> </output> </test> @@ -292,6 +291,11 @@ Such files can be produced with SnpSift Extract Fields and can be useful if preprocessing of the lists with standard text processing tools is required. + .. class:: infomark + + To represent empty EFF fields in the tabular format you can choose between + ``.`` and the empty string. + ---- Example output: