<commit_before><tool id="circgraph" name="circgraph" version="0.1.0">
<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>
    <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>
    </inputs>
    <outputs>
	<data format="txt" name="Default" label="PreCircos Datadump"/>
    </outputs>
    <help><![CDATA[
        Work in progress...
    ]]></help>
</tool>
<commit_msg>whitespace fixes<commit_after><tool id="circgraph" name="circgraph" version="0.1.0">
<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>
    <command detect_errors="aggressive" ><![CDATA[cp $circtmpxml $Default]]></command>
    <inputs>
    <!-- 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"/>
    </outputs>
    <help><![CDATA[
Circos Graphic
==============

Work in progress...
    ]]></help>
</tool>

{'fraction_non_alphanumeric': 0.17204301075268819, 'fraction_numerical': 0.008064516129032258, 'mean_word_length': 3.3080820265379978, 'pattern_counts': {'":': 0, '<': 363, '<?xml version=': 0, '>': 363, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '564136', 'n_tokens_mistral': 5914, 'n_tokens_neox': 5393, 'n_words': 1259}