Mercurial > repos > iuc > circos
comparison 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 |
comparison
equal
deleted
inserted
replaced
| 3:a2b4b1b1a88e | 4:6d45ebe16927 |
|---|---|
| 329 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/> | 329 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/> |
| 330 <param name="bezier_radius" type="float" value="0.1" min="0" max="1" label="Bezier Radius" | 330 <param name="bezier_radius" type="float" value="0.1" min="0" max="1" label="Bezier Radius" |
| 331 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"/> | 331 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"/> |
| 332 | 332 |
| 333 <section name="advanced" title="Advanced Settings"> | 333 <section name="advanced" title="Advanced Settings"> |
| 334 <param name="zdepth" type="float" value="" optional="true" label="Z-depth" | 334 <expand macro="zdepth"/> |
| 335 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"/> | |
| 336 <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest" | 335 <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest" |
| 337 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"/> | 336 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"/> |
| 338 <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity" | 337 <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity" |
| 339 help="The bezier_radius_purity adjusts the position of p2 for each link. The p2 control point will move along the line formed by the original p2 location and the intersection of p0-p1 and the bisecting radius. When purity = 1, p2' = p2. When purity = 0, p2' = midpoint(p0,p1)"/> | 338 help="The bezier_radius_purity adjusts the position of p2 for each link. The p2 control point will move along the line formed by the original p2 location and the intersection of p0-p1 and the bisecting radius. When purity = 1, p2' = p2. When purity = 0, p2' = midpoint(p0,p1)"/> |
| 340 <conditional name="perturbation"> | 339 <conditional name="perturbation"> |
| 432 <param name="bands" type="data" format="tabular" optional="true" label="Cytogenetic Bands" | 431 <param name="bands" type="data" format="tabular" optional="true" label="Cytogenetic Bands" |
| 433 help="If defined, will display cytogenetic bands as part of the karyotype configuration. This field accepts any tabular format file. If you provide a BED file you should enable automatic conversion below. Otherwise disable conversion below and it is expected that your file have 7 columns: 'band', chromosome ID (should match fasta), band ID, band ID (again), start, end, color (gneg, gpos, or r,g,b triple). E.g. a complete row would look like: 'band chr1 p32.2 p32.2 56100000 59000000 gneg25'"/> | 432 help="If defined, will display cytogenetic bands as part of the karyotype configuration. This field accepts any tabular format file. If you provide a BED file you should enable automatic conversion below. Otherwise disable conversion below and it is expected that your file have 7 columns: 'band', chromosome ID (should match fasta), band ID, band ID (again), start, end, color (gneg, gpos, or r,g,b triple). E.g. a complete row would look like: 'band chr1 p32.2 p32.2 56100000 59000000 gneg25'"/> |
| 434 <param name="convert_bands" type="boolean" truevalue="yes" falsevalue="no" label="Convert bands from BED format to circos karyotype band format" checked="true" | 433 <param name="convert_bands" type="boolean" truevalue="yes" falsevalue="no" label="Convert bands from BED format to circos karyotype band format" checked="true" |
| 435 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."/> | 434 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."/> |
| 436 <param name="fill_bands" type="boolean" truevalue="yes" falsevalue="no" label="Fill Bands" checked="true"/> | 435 <param name="fill_bands" type="boolean" truevalue="yes" falsevalue="no" label="Fill Bands" checked="true"/> |
| 437 <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"/> | 436 <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"/> |
| 438 | 437 |
| 439 <param type="integer" value="2" label="Band Stroke Thickness" name="band_stroke_thickness"/> | 438 <param type="integer" value="2" label="Band Stroke Thickness" name="band_stroke_thickness"/> |
| 440 <expand macro="circos_color" label="Band Stroke Color" name="band_stroke_color" value="#000000"/> | 439 <expand macro="circos_color" label="Band Stroke Color" name="band_stroke_color" value="#000000"/> |
| 441 </section> | 440 </section> |
| 442 </section> | 441 </section> |
| 483 <repeat name="data" title="Highlight" help="Highlights can help highlight a specific region by placing a large coloured block under some interesting or important features that the audience's eyes should be drawn towards"> | 482 <repeat name="data" title="Highlight" help="Highlights can help highlight a specific region by placing a large coloured block under some interesting or important features that the audience's eyes should be drawn towards"> |
| 484 <param name="r1" type="float" value="0.89" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/> | 483 <param name="r1" type="float" value="0.89" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/> |
| 485 <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)"/> | 484 <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)"/> |
| 486 <param name="data_source" type="data" format="tabular,interval" label="Highlight Data Source" help="Columns must be (chrom, start, end)"/> | 485 <param name="data_source" type="data" format="tabular,interval" label="Highlight Data Source" help="Columns must be (chrom, start, end)"/> |
| 487 <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#000000"/> | 486 <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#000000"/> |
| 487 <expand macro="stroke_opts"/> | |
| 488 <expand macro="zdepth"/> | |
| 488 <expand macro="rules" /> | 489 <expand macro="rules" /> |
| 489 </repeat> | 490 </repeat> |
| 490 </section> | 491 </section> |
| 491 | 492 |
| 492 <section name="outputs" title="Outputs"> | 493 <section name="outputs" title="Outputs"> |