Mercurial > repos > eric-rasche > circos
changeset 5:b25b3518c2ce draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2
| author | eric-rasche |
|---|---|
| date | Sat, 10 Jun 2017 12:55:28 -0400 |
| parents | 4ff5ff4c84fa |
| children | 169adf243c0a |
| files | README.rst circgraph.xml macros.xml macros_conffiles.xml unified-histogram.py unified-tiles.py |
| diffstat | 6 files changed, 24 insertions(+), 14 deletions(-) [+] |
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--- a/README.rst Sun Mar 05 17:02:17 2017 -0500 +++ b/README.rst Sat Jun 10 12:55:28 2017 -0400 @@ -31,13 +31,13 @@ - [x] Scatter Plots - [x] Line Plots -- [ ] Links +- [x] Links - [x] Axes - [x] Backgrounds -- [ ] Highlights +- [x] Highlights - [ ] Wedge +- [x] Test cases - [ ] Grids? -- [x] Test cases - [ ] Fine grained Z-depth control
--- a/circgraph.xml Sun Mar 05 17:02:17 2017 -0500 +++ b/circgraph.xml Sat Jun 10 12:55:28 2017 -0400 @@ -106,7 +106,7 @@ help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/> </section> <!-- TODO: multiple band files? --> - <param name="bands" type="data" format="bed6,bed12,gff3" optional="true" label="Cytogenetic Bands" + <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands" help="If defined, will display cytogenetic bands as part of the karyotype configuration"/> </section>
--- a/macros.xml Sun Mar 05 17:02:17 2017 -0500 +++ b/macros.xml Sat Jun 10 12:55:28 2017 -0400 @@ -3,9 +3,11 @@ <token name="@WRAPPER_VERSION@">0.9-RC1</token> <xml name="requirements"> <requirements> + <requirement type="package" version="0.69.4">circos</requirement> + <requirement type="package" version="2.2.3">libgd</requirement> <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="0.6.2">bcbiogff</requirement> - <requirement type="package" version="0.69.2">circos</requirement> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + <requirement type="package" version="1.67">biopython</requirement> </requirements> </xml> @@ -165,6 +167,7 @@ <option value="fill_color">Change Fill Color for all points</option> <option value="fill_color_value">Change Fill Color based on Value</option> <option value="color">Change Stroke Color</option> + <option value="color_value">Change Stroke Color based on Value</option> </param> <when value="show"> <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/> @@ -180,6 +183,11 @@ <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> </when> + <when value="color_value"> + <expand macro="brewer_scale" name="action_value" label="Stroke Color"/> + <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> + <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> + </when> </conditional> </repeat> <param name="continue_flow" type="boolean" truevalue="flow = continue" falsevalue="" label="Continue flow"
--- a/macros_conffiles.xml Sun Mar 05 17:02:17 2017 -0500 +++ b/macros_conffiles.xml Sat Jun 10 12:55:28 2017 -0400 @@ -170,7 +170,7 @@ #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1 #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.action_value, $i) for i in range(1, $x_fill_color_count)]) - #if str($action.action.action_select) == "fill_color_value": + #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" : fill_color = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, 0, ${x_fill_color_count - 1})]) #else $action.action.action_select = ${action.action.action_value} @@ -328,7 +328,9 @@ <configfile name="test_case_conf"><![CDATA[ <!-- mkdir -p test-data/my-test-case/; -cp ${genome_fasta} test-data/my-test-case/input.fa; +#if $reference_genome.reference_genome_source == 'history': + cp ${genome_fasta} test-data/my-test-case/input.fa; +#end if #if $ideogram.bands: cp ${ideogram.bands} test-data/my-test-case/bands.${ideogram.bands.ext}; #end if
--- a/unified-histogram.py Sun Mar 05 17:02:17 2017 -0500 +++ b/unified-histogram.py Sat Jun 10 12:55:28 2017 -0400 @@ -116,7 +116,7 @@ # histogram # hs4 0 1999999 5.0000,3.0000,1.0000,19.0000 sys.stdout.write(' '.join( - (genome, region_start, region_end, ','.join(values)) + (genome, str(region_start), str(region_end), ','.join(map(str, values))) ) + '\n') elif MODE == 'heatmap': # heatmap @@ -129,21 +129,21 @@ for x in max_idx: if x in data[genome][position]: sys.stdout.write(' '.join( - (genome, region_start, region_end, data[genome][position][x], 'id=hm%s' % x) + (genome, str(region_start), str(region_end), data[genome][position][x], 'id=hm%s' % x) ) + '\n') else: sys.stdout.write(' '.join( - (genome, region_start, region_end, 0.0, 'id=hm%s' % x) + (genome, str(region_start), str(region_end), 0.0, 'id=hm%s' % x) ) + '\n') elif MODE == 'line': # multiple=False sys.stdout.write(' '.join( - (genome, region_start, region_end, data[genome][position][0]) + (genome, str(region_start), str(region_end), data[genome][position][0]) ) + '\n') elif MODE == 'scatter': # multiple=False sys.stdout.write(' '.join( - (genome, region_start, region_end, data[genome][position][0]) + (genome, str(region_start), str(region_end), data[genome][position][0]) ) + '\n') # Update start of next array
--- a/unified-tiles.py Sun Mar 05 17:02:17 2017 -0500 +++ b/unified-tiles.py Sat Jun 10 12:55:28 2017 -0400 @@ -68,4 +68,4 @@ if item[6] is not None: lineExtra.append('color=%s' % item[6]) - sys.stdout.write(' '.join((item[0], item[1], item[2], ','.join(lineExtra))) + '\n') + sys.stdout.write(' '.join((str(item[0]), str(item[1]), str(item[2]), ','.join(lineExtra))) + '\n')