Mercurial > repos > iuc > circos
changeset 12:290a11559985 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit e3d1aad2204a3385aa66f3b0625747151e9f94e8"
| author | iuc |
|---|---|
| date | Mon, 22 Nov 2021 12:23:12 +0000 |
| parents | 31a35811dda6 |
| children | c4bde687c846 |
| files | circos.xml macros.xml macros_tests.xml tableviewer.xml |
| diffstat | 4 files changed, 52 insertions(+), 8 deletions(-) [+] |
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--- a/circos.xml Tue Nov 16 09:20:08 2021 +0000 +++ b/circos.xml Mon Nov 22 12:23:12 2021 +0000 @@ -608,12 +608,7 @@ </section> - <section name="limits" title="Limits"> - <param name="max_ticks" type="integer" min="200" value="5000" label="Maximum number of ticks to draw" help="These are advanced options, if you increase these due to a plotting failure it may result in a significantly longer plotting time. Beware!"/> - <param name="max_ideograms" type="integer" min="200" value="200" label="Maximum number of ideograms to draw"/> - <param name="max_links" type="integer" min="200" value="25000" label="Maximum number of links to draw"/> - <param name="max_points_per_track" type="integer" min="200" value="25000" label="Maximum number of points per track"/> - </section> + <expand macro="limits" /> <section name="outputs" title="Outputs"> <param name="png" type="boolean" truevalue="yes" falsevalue="no" label="PNG" checked="true"/>
--- a/macros.xml Tue Nov 16 09:20:08 2021 +0000 +++ b/macros.xml Mon Nov 22 12:23:12 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">0.69.8</token> - <token name="@VERSION_SUFFIX@">9</token> + <token name="@VERSION_SUFFIX@">10</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token> @@ -566,4 +566,13 @@ </conditional> </xml> + <xml name="limits"> + <section name="limits" title="Limits"> + <param name="max_ticks" type="integer" min="200" value="5000" label="Maximum number of ticks to draw" help="These are advanced options, if you increase these due to a plotting failure it may result in a significantly longer plotting time. Beware!"/> + <param name="max_ideograms" type="integer" min="200" value="200" label="Maximum number of ideograms to draw"/> + <param name="max_links" type="integer" min="200" value="25000" label="Maximum number of links to draw"/> + <param name="max_points_per_track" type="integer" min="200" value="25000" label="Maximum number of points per track"/> + </section> + </xml> + </macros>
--- a/macros_tests.xml Tue Nov 16 09:20:08 2021 +0000 +++ b/macros_tests.xml Mon Nov 22 12:23:12 2021 +0000 @@ -18,6 +18,31 @@ <output name="output_png" file="0/out.png" compare="sim_size" delta="15000" ftype="png"/> <output name="output_svg" file="0/out.svg" compare="sim_size" delta="15000" ftype="svg"/> </test> + + <test expect_failure="true"> + <section name="reference_genome"> + <conditional name="ref"> + <param name="ref_source" value="history" /> + <param name="genome_fasta" value="1/input.fa" /> + </conditional> + </section> + + <section name="outputs"> + <param name="png" value="yes" /> + <param name="svg" value="yes" /> + </section> + + <section name="limits"> + <param name="max_ticks" value="1" /> + <param name="max_ideograms" value="1" /> + <param name="max_links" value="1" /> + <param name="max_points_per_track" value="1" /> + </section> + + <output name="output_png" file="0/out.png" compare="sim_size" delta="15000" ftype="png"/> + <output name="output_svg" file="0/out.svg" compare="sim_size" delta="15000" ftype="svg"/> + </test> + <test> <section name="reference_genome"> <conditional name="ref">
--- a/tableviewer.xml Tue Nov 16 09:20:08 2021 +0000 +++ b/tableviewer.xml Mon Nov 22 12:23:12 2021 +0000 @@ -586,7 +586,11 @@ <<include etc/colors_fonts_patterns.conf>> <<include etc/housekeeping.conf>> - ]]></configfile> +max_ticks* = ${limits.max_ticks} +max_ideograms* = ${limits.max_ideograms} +max_links* = ${limits.max_links} +max_points_per_track* = ${limits.max_points_per_track} +]]></configfile> </configfiles> <inputs> <param name="table" type="data" format="tabular" label="Input table"/> @@ -612,6 +616,8 @@ <expand macro="circos_color" label="Color" name="color" value="#000000" /> </section> </section> + + <expand macro="limits" /> </inputs> <outputs> <data name="output_png" format="png" from_work_dir="circos.png" label="Circos TableViewer Plot"> @@ -629,6 +635,15 @@ <param name="table" value="tableviewer/1.tab" ftype="tabular" /> <output name="output_png" file="tableviewer/1.png" ftype="png" compare="sim_size" delta="90000" /> </test> + <test expect_failure="true"> + <param name="table" value="tableviewer/1.tab" ftype="tabular" /> + <section name="limits"> + <param name="max_ticks" value="1" /> + <param name="max_ideograms" value="1" /> + <param name="max_links" value="1" /> + <param name="max_points_per_track" value="1" /> + </section> + </test> </tests> <help><![CDATA[ The `official documentation <http://mkweb.bcgsc.ca/tableviewer/docs/>`__ has a lot of useful information.