Mercurial > repos > eric-rasche > circos
changeset 8:eb3af6e9f633 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474
| author | eric-rasche |
|---|---|
| date | Sat, 10 Jun 2017 16:21:01 -0400 |
| parents | b72f2db6d417 |
| children | e6440d0201f7 |
| files | circgraph.xml macros.xml macros_conffiles.xml |
| diffstat | 3 files changed, 26 insertions(+), 14 deletions(-) [+] |
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--- a/circgraph.xml Sat Jun 10 14:16:41 2017 -0400 +++ b/circgraph.xml Sat Jun 10 16:21:01 2017 -0400 @@ -24,8 +24,8 @@ genomeref.fa #end if - #if $ideogram.bands: - "${ideogram.bands}" + #if $reference_genome.bands: + "${reference_genome.bands}" #end if > circos/conf/karyotype.txt && #else
--- a/macros.xml Sat Jun 10 14:16:41 2017 -0400 +++ b/macros.xml Sat Jun 10 16:21:01 2017 -0400 @@ -182,11 +182,13 @@ <expand macro="brewer_scale" name="action_value" label="Fill 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"/> + <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" /> </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"/> + <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" /> </when> </conditional> </repeat> @@ -281,6 +283,7 @@ <expand macro="brewer_scale" label="Fill Color" name="action_value"/> <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"/> + <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" /> </when> </conditional> </when>
--- a/macros_conffiles.xml Sat Jun 10 14:16:41 2017 -0400 +++ b/macros_conffiles.xml Sat Jun 10 16:21:01 2017 -0400 @@ -166,12 +166,13 @@ #end for #for $action in $rule.actions: - #set x_fill_color = $action.action.action_value - #set x_fill_color_count = int(str($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" or str($action.action.action_select) == "color_value" : + #set x_fill_color = $action.action.action_value + #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + #set x_min = $x_fill_color_count if $action.action.invert else 1 + #set x_max = 1 if $action.action.invert else $x_fill_color_count - #if str($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, ${x_fill_color_count - 1})]) + fill_color = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max}))) #else $action.action.action_select = ${action.action.action_value} #end if @@ -284,9 +285,11 @@ $actiontype = $actionval #else #set x_fill_color = $action.action.dynamic.action_value - #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1 - #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.dynamic.action_value, $i) for i in range(1, $x_fill_color_count)]) - $actiontype = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, 0, ${x_fill_color_count - 1})]) + #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1 + #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count + + $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))) #end if #else #set actionval = $action.action.action_value @@ -342,9 +345,13 @@ #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}; + +#if $reference_genome.reference_genome_source != 'karyotype': +#if $reference_genome.bands: +cp ${reference_genome.bands} test-data/my-test-case/bands.${reference_genome.bands.ext}; #end if +#end if + #for $idx, $data in enumerate($sec_tdd.data): #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'): #for $jdx, $file in enumerate($data.plot_format.data_source): @@ -366,8 +373,10 @@ <param name="ideogram|thickness" value="${ideogram.thickness}" /> <param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" /> <param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" /> - #if $ideogram.bands: - <param name="ideogram|bands" value="my-test-case/bands.${ideogram.bands.ext}" /> + #if $reference_genome.reference_genome_source != 'karyotype': + #if $reference_genome.bands: + <param name="reference_genome.bands" value="my-test-case/bands.${reference_genome.bands.ext}" /> + #end if #end if <!-- Ticks --> <param name="ticks|show_ticks" value="${ticks.show_ticks}" />