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Merge pull request #5 from stephencrosby/whitespace
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whitespace fixes
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@stcrosby9293
stcrosby9293 committed Oct 29, 2015
2 parents 56f932e + ab6515c commit c287de3
Showing 1 changed file with 154 additions and 164 deletions.
318 changes: 154 additions & 164 deletions circgraph.xml
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Original file line number Diff line number Diff line change
@@ -1,178 +1,168 @@
<tool id="circgraph" name="circgraph" version="0.1.0">
<description> for making Circos graphics. </description>
<description>for making Circos graphics.</description>
<requirements>
<requirement type="package">circgraph</requirement>
<requirement type="package">Bio</requirement>
<requirement type="package">BCBio</requirement>
</requirements>
<configfiles>
<configfile name="circtmpxml"><![CDATA[
<image>
<bcolor> ${imgback} </bcolor>
</image>
#for $seq in $base_sequences:
#for $ideogram in $seq.ideograms:
#for $element in $ideogram.items():
#if $element[0] not in ('source_data')
<$element[0]> $element[1] </$element[0]>
#end if
#end for
#for $track in $ideogram.source_data:
#for $key in $track.data_type.items():
<$key[0]> $key[1] </$key[0]>
#end for
#for $key in $track.track_opt.items():
<$key[0]> $key[1] </$key[0]>
#end for
#end for
#end for
#for $highlight in $seq.highlights:
#for $element in $highlight.items():
<$element[0]> $element[1] </$element[0]>
#end for
#end for
#for $tick in $seq.ticks:
#for $element in $tick.items():
<$element[0]> $element[1] </$element[0]>
#end for
#end for
#end for
]]>
</configfile>
</configfiles>
<configfiles>
<configfile name="circtmpxml"><![CDATA[
<image>
<bcolor>${imgback}</bcolor>
</image>
#for $seq in $base_sequences:
#for $ideogram in $seq.ideograms:
#for $element in $ideogram.items():
#if $element[0] not in ('source_data')
<$element[0]>$element[1]</$element[0]>
#end if
#end for
#for $track in $ideogram.source_data:
#for $key in $track.data_type.items():
<$key[0]>$key[1]</$key[0]>
#end for
#for $key in $track.track_opt.items():
<$key[0]>$key[1]</$key[0]>
#end for
#end for
#end for
#for $highlight in $seq.highlights:
#for $element in $highlight.items():
<$element[0]>$element[1]</$element[0]>
#end for
#end for
#for $tick in $seq.ticks:
#for $element in $tick.items():
<$element[0]>$element[1]</$element[0]>
#end for
#end for
#end for
]]>
</configfile>
</configfiles>
<command detect_errors="aggressive" ><![CDATA[cp $circtmpxml $Default]]></command>
<inputs>
<param name="imgback" title="Background Color" type="color">
<option value="white" selected="True"> White</option>
<option value="black"> Black </option>
<option value="grey"> Grey </option>
</param>
<repeat name="base_sequences" title="Genome" min="1" max="10">
<repeat name="highlights" title="Highlight">
<param type="data" format="txt" name="HighlightData" />
<param type="color" label="Fill Color" name="hilite_fill" />
<option value="red" selected="True"> Red </option>
<param type="color" label="Stroke Color" name="hilite_stroke" />
<option value="red" selected="True"> Red </option>
<param type="float" value="0.5" label="Inner Radial Position" name="hilite_r0" />
<param type="float" value="1" label="Outer Radial Position" name="hilite_r1" />
<param type="float" value="1" label="Depth" name="hilite_z" />
<param type="float" value="1" label="Stroke Thickness" name="hilite_stroke_thickness" />
</repeat>
<repeat name="ticks" title="Tick">
<param type="text" value="Chr1;Chr2" label="Chromosomes" name="tick_chromosomes" />
<param type="color" value="1" label="Color" name="tick_color" />
<option value="red" selected="True"> Red </option>
<param type="boolean" checked="true" label="Force Display?" name="tick_force_display" />
<param type="text" value="%.2f" label="Format" name="tick_format" />
<param type="boolean" checked="true" label="Grid?" name="tick_grid" />
<param type="color" value="1" label="Grid Color" name="tick_grid_color" />
<option value="red" selected="True"> Red </option>
<param type="float" value="1" label="Grid Start" name="tick_grid_start" />
<param type="float" value="2" label="Grid End" name="tick_grid_end" />
<param type="float" value="1" label="Grid Thickness" name="tick_grid_thickness" />
<param type="boolean" checked="true" label="Label?" name="tick_label" />
<param type="color" value="1" label="Label Color" name="tick_label_color" />
<option value="red" selected="True"> Red </option>
<param type="float" value="1" label="Label Relative" name="tick_label_relative" />
<param type="float" value="1" label="Label Separation" name="tick_label_separation" />
<param type="float" value="1" label="Label Size" name="tick_label_size" />
<param type="float" value="1" label="Minimum Distance to Edge" name="tick_min_distance_to_edge" />
<param type="float" value="1" label="Minimum Label Distance to Edge" name="tick_min_label_distance_to_edge" />
<param type="text" value="0p" label="Offset" name="tick_offset" />
<param type="float" value="1" label="Position" name="tick_position" />
<param type="text" value="Not Yet Implemented!" label="Prefix" name="tick_prefix" />
<param type="float" value="1" label="Radius" name="tick_radius" />
<param type="boolean" checked="true" label="Show Label?" name="tick_show_label" />
<param type="float" value="1" label="Size" name="tick_size" />
<param type="boolean" checked="false" label="Skip First Label?" name="tick_skip_first_label" />
<param type="boolean" checked="false" label="Skip Last Label?" name="tick_skip_last_label" />
<param type="float" value="1" label="Thickness" name="tick_thickness" />
<param type="float" value="1" label="Thousands Separation" name="tick_thousands_sep" />
<param type="float" value="1" label="Tick Separation" name="tick_separation" />
</repeat>
<repeat name="ideograms" title="Ideogram" min="1" max="10">
<param name="idname" type="text" value="Ideogram1" help="Create a distinct Circos ideogram"/>
<param type="color" label="Band Color" name="band_stroke_color">
<option value="red" selected="True"> Red </option>
</param>
<param type="float" value="1" label="Band Thickness" name="band_stroke_thickness">
</param>
<param type="float" value="1" label="Band Transparency" name="band_stroke_transparency">
</param>
<param type="boolean" checked="true" label="Fill?" name="ideo_fill" />
<param type="boolean" checked="false" label="Fill with bands?" name="ideo_fill_bands" />
<param type="color" label="Fill Color" name="ideo_fill_color" >
<option value="red" selected="True"> Red </option>
</param>
<param type="select" label="Label Case" name="ideo_label_case" >
<option value="Lower" selected="True"> Red </option>
<option value="Upper" selected="True"> Red </option>
</param>
<param type="boolean" checked="true" label="Center Label?" name="ideo_label_center" />
<param type="select" label="Label Font" name="ideo_label_font" >
<option value="Times New Roman" selected="True"> Red </option>
</param>
<param type="select" label="Label Format" name="ideo_label_format" >
<option value="TODO" selected="True"> Red </option>
</param>
<param type="boolean" checked="true" label="Labels Parallel?" name="ideo_label_parallel" />
<param type="float" value="1" label="Label Radius" name="ideo_label_radius" />
<param type="float" value="1" label="Label Size" name="ideo_label_size" />
<param type="boolean" checked="false" label="Label with tag?" name="ideo_tag_label_with_tag" />
<param type="float" value="1" label="Radius" name="ideo_radius" />
<param type="float" value="1" label="Stroke Thickness" name="ideo_stroke_thickness" />
<param type="color" label="Stroke Color" name="ideo_stroke_color" >
<option value="red" selected="True"> Red </option>
</param>
<param type="float" value="1" label="Thickness" name="ideo_thickness" />
<repeat name="source_data" title="Data Tracks">
<conditional name="data_type" label="Data Type Selection">
<param type="select" label="Data Type" name="datatype">
<option value="gff3" selected="True"> gff3 </option>
<option value="wig"> wig </option>
<option value="fasta"> fasta </option>
</param>
<when value="gff3">
<param type="data" name="gff3" format="gff3"/>
</when>
<when value="wig">
<param type="data" name="wig" format="wig"/>
</when>
<when value="fasta">
<param type="data" name="fasta" format="fa"/>
</when>
</conditional>
<conditional name="track_opt" label="Track Selection">
<param type="select" label="Track Type" name="tracktype">
<option value="Scatterplot" selected="True"> Scatterplot </option>
<option value="Heatmap"> Heatmap </option>
<option value="Histogram"> Histogram </option>
</param>
<when value="Heatmap">
<param label="Colorscheme" type="select" name="color">
<option value="Brewer1" selected="True"> Brewer Palette 1 </option>
<option value="Brewer2"> Brewer Palette 2 </option>
<option value="Brewer3"> Brewer Palette 3 </option>
</param>
</when>
<when value="Scatterplot"> </when>
<when value="Histogram">
<param label="Color" type="color" name="color">
<option value="red" selected="True"> Red </option>
<option value="orange"> Orange </option>
<option value="yellow"> Yellow </option>
</param>
</when>
</conditional>
</repeat>
</repeat>
</repeat>
<!-- Pretty sure this is how you set defaults -->
<param name="imgback" title="Background Color" type="color" default="#ffffff"/>
<repeat name="base_sequences" title="Genome" min="1" max="10">
<repeat name="highlights" title="Highlight">
<param type="data" format="txt" name="HighlightData" />
<param type="color" label="Fill Color" name="hilite_fill" />
<param type="color" label="Stroke Color" name="hilite_stroke" />
<param type="float" value="0.5" label="Inner Radial Position" name="hilite_r0" />
<param type="float" value="1" label="Outer Radial Position" name="hilite_r1" />
<param type="float" value="1" label="Depth" name="hilite_z" />
<param type="float" value="1" label="Stroke Thickness" name="hilite_stroke_thickness" />
</repeat>
<repeat name="ticks" title="Tick">
<param type="text" value="Chr1;Chr2" label="Chromosomes" name="tick_chromosomes" />
<param type="color" value="1" label="Color" name="tick_color" />
<param type="boolean" checked="true" label="Force Display?" name="tick_force_display" />
<param type="text" value="%.2f" label="Format" name="tick_format" />
<param type="boolean" checked="true" label="Grid?" name="tick_grid" />
<param type="color" value="1" label="Grid Color" name="tick_grid_color" />
<param type="float" value="1" label="Grid Start" name="tick_grid_start" />
<param type="float" value="2" label="Grid End" name="tick_grid_end" />
<param type="float" value="1" label="Grid Thickness" name="tick_grid_thickness" />
<param type="boolean" checked="true" label="Label?" name="tick_label" />
<param type="color" value="1" label="Label Color" name="tick_label_color" />
<param type="float" value="1" label="Label Relative" name="tick_label_relative" />
<param type="float" value="1" label="Label Separation" name="tick_label_separation" />
<param type="float" value="1" label="Label Size" name="tick_label_size" />
<param type="float" value="1" label="Minimum Distance to Edge" name="tick_min_distance_to_edge" />
<param type="float" value="1" label="Minimum Label Distance to Edge" name="tick_min_label_distance_to_edge" />
<param type="text" value="0p" label="Offset" name="tick_offset" />
<param type="float" value="1" label="Position" name="tick_position" />
<param type="text" value="Not Yet Implemented!" label="Prefix" name="tick_prefix" />
<param type="float" value="1" label="Radius" name="tick_radius" />
<param type="boolean" checked="true" label="Show Label?" name="tick_show_label" />
<param type="float" value="1" label="Size" name="tick_size" />
<param type="boolean" checked="false" label="Skip First Label?" name="tick_skip_first_label" />
<param type="boolean" checked="false" label="Skip Last Label?" name="tick_skip_last_label" />
<param type="float" value="1" label="Thickness" name="tick_thickness" />
<param type="float" value="1" label="Thousands Separation" name="tick_thousands_sep" />
<param type="float" value="1" label="Tick Separation" name="tick_separation" />
</repeat>
<repeat name="ideograms" title="Ideogram" min="1" max="10">
<param name="idname" type="text" value="Ideogram1" help="Create a distinct Circos ideogram"/>
<param type="color" label="Band Color" name="band_stroke_color"/>
<param type="float" value="1" label="Band Thickness" name="band_stroke_thickness">
</param>
<param type="float" value="1" label="Band Transparency" name="band_stroke_transparency">
</param>
<param type="boolean" checked="true" label="Fill?" name="ideo_fill" />
<param type="boolean" checked="false" label="Fill with bands?" name="ideo_fill_bands" />
<param type="color" label="Fill Color" name="ideo_fill_color" />
<param type="select" label="Label Case" name="ideo_label_case" >
<option value="Lower" selected="True">lower case</option>
<option value="Upper">Upper Case</option>
</param>
<param type="boolean" checked="true" label="Center Label?" name="ideo_label_center" />
<param type="select" label="Label Font" name="ideo_label_font" >
<option value="Times New Roman" selected="True"> Red </option>
</param>
<param type="select" label="Label Format" name="ideo_label_format" >
<option value="TODO" selected="True"> Red </option>
</param>
<param type="boolean" checked="true" label="Labels Parallel?" name="ideo_label_parallel" />
<param type="float" value="1" label="Label Radius" name="ideo_label_radius" />
<param type="float" value="1" label="Label Size" name="ideo_label_size" />
<param type="boolean" checked="false" label="Label with tag?" name="ideo_tag_label_with_tag" />
<param type="float" value="1" label="Radius" name="ideo_radius" />
<param type="float" value="1" label="Stroke Thickness" name="ideo_stroke_thickness" />
<param type="color" label="Stroke Color" name="ideo_stroke_color" />
<param type="float" value="1" label="Thickness" name="ideo_thickness" />
<repeat name="source_data" title="Data Tracks">
<conditional name="data_type" label="Data Type Selection">
<param type="select" label="Data Type" name="datatype">
<option value="gff3" selected="True"> gff3 </option>
<option value="wig"> wig </option>
<option value="fasta"> fasta </option>
</param>
<when value="gff3">
<param type="data" name="gff3" format="gff3"/>
</when>
<when value="wig">
<param type="data" name="wig" format="wig"/>
</when>
<when value="fasta">
<param type="data" name="fasta" format="fa"/>
</when>
</conditional>
<conditional name="track_opt" label="Track Selection">
<param type="select" label="Track Type" name="tracktype">
<option value="Scatterplot" selected="True">Scatterplot</option>
<option value="Heatmap">Heatmap</option>
<option value="Histogram">Histogram</option>
</param>
<when value="Heatmap">
<param label="Colorscheme" type="select" name="color">
<option value="Brewer1" selected="True">Brewer Palette 1</option>
<option value="Brewer2">Brewer Palette 2</option>
<option value="Brewer3">Brewer Palette 3</option>
</param>
</when>
<when value="Scatterplot"> </when>
<when value="Histogram">
<param label="Color" type="color" name="color"/>
</when>
</conditional>
</repeat>
</repeat>
</repeat>
</inputs>
<outputs>
<data format="txt" name="Default" label="PreCircos Datadump"/>
<data format="txt" name="Default" label="PreCircos Datadump"/>
</outputs>
<help><![CDATA[
Work in progress...
Circos Graphic
==============
Work in progress...
]]></help>
</tool>

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