Mercurial > repos > iuc > circos
diff circos.xml @ 4:6d45ebe16927 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"
| author | iuc |
|---|---|
| date | Thu, 09 Jan 2020 15:02:34 +0000 |
| parents | a2b4b1b1a88e |
| children | b84d385679e2 |
line wrap: on
line diff
--- a/circos.xml Mon Dec 02 13:13:27 2019 +0000 +++ b/circos.xml Thu Jan 09 15:02:34 2020 +0000 @@ -331,8 +331,7 @@ help="The radial position of the third control point (in addition to the two positions defined by the link coordinates) used to draw the Bezier curve; if this parameter is 0 then straight lines will be used"/> <section name="advanced" title="Advanced Settings"> - <param name="zdepth" type="float" value="" optional="true" label="Z-depth" - help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple link tracks"/> + <expand macro="zdepth"/> <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest" help="Two additional Bezier control points can be set by using the crest parameter. When defined, points p3 and p4 are added. These points lie at the same angular position as the start and end link termini and have the radial position. In the crest=0 extreme, p3 and p4 are at the same position as p0,p1. In this case, crest has no effect. When crest=1, p3,p4 are at the radial position of p2, the control point set by bezier_radius"/> <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity" @@ -434,7 +433,7 @@ <param name="convert_bands" type="boolean" truevalue="yes" falsevalue="no" label="Convert bands from BED format to circos karyotype band format" checked="true" help="Automatically reformat BED file into the appropriate columns. This should be a BED 6+ file, BED 9+ if you want the colours from the BED file automatically used. Otherwise everything will appear grey."/> <param name="fill_bands" type="boolean" truevalue="yes" falsevalue="no" label="Fill Bands" checked="true"/> - <param name="band_transparency" type="integer" label="Fill Bands" value="0" min="0" max="5" help="0 is solid, 1 is the least transparent, and 5 is the most transparent"/> + <param name="band_transparency" type="integer" label="Band Transparency" value="0" min="0" max="5" help="0 is solid, 1 is the least transparent, and 5 is the most transparent"/> <param type="integer" value="2" label="Band Stroke Thickness" name="band_stroke_thickness"/> <expand macro="circos_color" label="Band Stroke Color" name="band_stroke_color" value="#000000"/> @@ -485,6 +484,8 @@ <param name="r0" type="float" value="0.8" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/> <param name="data_source" type="data" format="tabular,interval" label="Highlight Data Source" help="Columns must be (chrom, start, end)"/> <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#000000"/> + <expand macro="stroke_opts"/> + <expand macro="zdepth"/> <expand macro="rules" /> </repeat> </section>
