view macros_conffiles.xml @ 9:e6440d0201f7 draft default tip

planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7e335df423e3e06da3d33a5378a336a149e6cc6c

<?xml version="1.0"?>
<macros>
  <xml name="configfile_circos_conf">
    <configfile name="circos_conf"><![CDATA[
<<include colors_fonts_patterns.conf>>
<<include housekeeping.conf>>
karyotype = karyotype.txt

<image>
  <<include etc/image.conf>>
</image>

<<include ticks.conf>>
<<include ideogram.conf>>
<plots>
    <<include 2d.conf>>
    <<include plot_highlight.conf>>
</plots>
<links>
    <<include links.conf>>
</links>

<<include highlight.conf>>
    ]]></configfile>
  </xml>
  <xml name="configfile_ticks_conf">
    <configfile name="ticks_conf"><![CDATA[
show_ticks          = ${ticks.show_ticks}
show_tick_labels    = yes

#def circosColor($value)
    #set $value = str($value)
    #set $r = int($value[1:3], 16)
    #set $g = int($value[3:5], 16)
    #set $b = int($value[5:], 16)
    $r, $g, $b
#end def


<ticks>
    radius           = ${ticks.radius}r
    color            = $circosColor($ticks.color)
    thickness        = 2p
    multiplier       = ${ticks.multiplier}

    #for $tick_group in $ticks.tick_group:
    <tick>
        spacing        = ${tick_group.spacing}
        size           = ${tick_group.size}p
        show_label     = ${tick_group.show_tick_labels}
        label_size     = ${tick_group.label_size}p
        label_offset   = ${tick_group.label_offset}p
        format         = ${tick_group.format} kb
        ## TODO: figure out automated tick labels
        ##if ${ticks.multiplier} * ${tick_group.spacing}
    </tick>
    #end for
</ticks>
]]>
    </configfile>
  </xml>
  <xml name="configfile_ideogram_conf">
    <configfile name="ideogram_conf"><![CDATA[

<ideogram>

    <spacing>
        ## spacing between ideograms
        default = ${ideogram.spacing}r
    </spacing>

    # ideogram position, thickness and fill
    radius           = ${ideogram.radius}r
    thickness        = ${ideogram.thickness}p
    fill             = yes

    show_label       = ${ideogram.ideogram_labels.show_label}
    label_radius     = dims(ideogram,radius) + 0.075r
    label_size       = 24
    label_parallel   = ${ideogram.ideogram_labels.parallel}

    show_bands            = yes
    fill_bands            = yes
    band_transparency     = 4

</ideogram>
]]></configfile>
  </xml>
  <xml name="configfile_data_conf">
    <configfile name="data_conf"><![CDATA[
#for $hi, $data in enumerate($sec_tdd.data):
<plot>
    #set plot_type = str($data.plot_format.plot_format_select)
    #def circosColor($value)
        #set $value = str($value)
        #set $r = int($value[1:3], 16)
        #set $g = int($value[3:5], 16)
        #set $b = int($value[5:], 16)
        $r, $g, $b
    #end def

    type = ${plot_type}
    file = data/data-${hi}.txt

    r1   = ${data.r1}r
    r0   = ${data.r0}r
    orientation = ${data.orientation}

#if str($plot_type) == 'histogram':
    extend_bin = ${data.plot_format.format_specific.extend_bins}
    fill_color = ${data.plot_format.format_specific.fill_color}
#else if str($plot_type) == 'heatmap':
    color = $circosColor($data.plot_format.format_specific.fill_color)
    scale_log_base = ${data.plot_format.format_specific.scale_log_base}
#else if str($plot_type) == 'line':
    color     = $circosColor($data.plot_format.format_specific.color)
    thickness = ${data.plot_format.format_specific.thickness}
#else if str($plot_type) == 'scatter':
    glyph                = ${data.plot_format.format_specific.glyph}
    glyph_size           = ${data.plot_format.format_specific.glyph_size}
    color                = $circosColor($data.plot_format.format_specific.color)
    stroke_color         = $circosColor($data.plot_format.format_specific.stroke_color)
    stroke_thickness     = ${data.plot_format.format_specific.stroke_thickness}
#else if str($plot_type) == 'tile':
    color                = ${data.plot_format.format_specific.color}
    stroke_color         = $circosColor($data.plot_format.format_specific.color)
    stroke_thickness     = ${data.plot_format.format_specific.stroke_thickness}
    layers               = ${data.plot_format.format_specific.layers}
    thickness            = ${data.plot_format.format_specific.thickness}
    padding              = ${data.plot_format.format_specific.padding}

    layers_overflow       = ${data.plot_format.format_specific.overflow.overflow_behavior}
    #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
    layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
    #end if
#end if

    <rules>
    #for $rule in $data.sec_rule.rules:
        <rule>
            #for $condition in $rule.conditions
                #if str($condition.application.application_select) == "1":
                    condition = 1
                #elif str($condition.application.application_select) == "on":
                    #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
                    condition = $on_str
                #elif str($condition.application.application_select) == "pos":
                    #if float($condition.application.pos_gt) != 0:
                    condition = var(start) > $condition.application.pos_gt
                    #end if

                    #if float($condition.application.pos_lt) != 0:
                    condition = var(start) < $condition.application.pos_lt
                    #end if
                #elif str($condition.application.application_select) == "value":
                    #if float($condition.application.pos_gt) != 0:
                    condition = var(value) > $condition.application.pos_gt
                    #end if

                    #if float($condition.application.pos_lt) != 0:
                    condition = var(value) < $condition.application.pos_lt
                    #end if
                #elif str($condition.application.application_select) == "var":
                    condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
                #end if
            #end for

            #for $action in $rule.actions:
                #if str($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 $x_fill_color_count
                    #set color_action = "fill_color" if str($plot_type) == 'histogram' else "color"

                    $color_action = eval(sprintf("${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
            #end for
            $rule.continue_flow
        </rule>
    #end for
    </rules>

    <axes>
        #for $axis in $data.sec_axes.axes:
        <axis>
            color     = $circosColor($axis.color)
            thickness = ${axis.thickness}
            spacing   = ${axis.spacing}r
            y0        = ${axis.y0}r
            y1        = ${axis.y1}r
        </axis>
        #end for
    </axes>
    <backgrounds>
        #for $bkg in $data.sec_bkgs.backgrounds:
        <background>
            color = $circosColor($bkg.color)
            y0    = ${bkg.y0}r
            y1    = ${bkg.y1}r
        </background>
        #end for
    </backgrounds>
</plot>
#end for
    ]]></configfile>
  </xml>

  <xml name="configfile_links_conf">
    <configfile name="links_conf"><![CDATA[
#for $hi, $data in enumerate($sec_links.data):
<link>
    #def circosColor($value)
        #set $value = str($value)
        #set $r = int($value[1:3], 16)
        #set $g = int($value[3:5], 16)
        #set $b = int($value[5:], 16)
        $r, $g, $b
    #end def

    file = data/links-${hi}.txt

    radius   = ${data.radius}r
    ribbon   = ${data.linktype.ribbon}
    #if $data.linktype.ribbon == 'yes'
        ${data.linktype.twist}
    #end if
    color                = $circosColor($data.color)
    bezier_radius        = ${data.bezier_radius}r
    thickness            = ${data.thickness}
    crest                = ${data.advanced.crest}
    bezier_radius_purity = ${data.advanced.bezier_radius_purity}

    #if $data.advanced.perturbation.perturb == 'yes'
        perturb = yes
        perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
        perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
        perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
    #end if

    #if $data.advanced.zdepth
        z = ${data.advanced.zdepth}
    #end if

    <rules>
    #for $rule in $data.sec_link_rule.rules:
        <rule>
            #for $condition in $rule.conditions
                #set cond = $condition.application.application_select
                #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
                    condition = var($cond)
                #elif $cond == 'always'
                    condition = 1
                #else
                    #set op = $condition.application.comparison.compare
                    #set val = $condition.application.comparison.compval
                    #if $cond == 'chr'
                        #if $op == 'between' or $op == 'fromto'
                            #set val2 = $condition.application.comparison.compval2
                            #set c=''.join([str($op),"(",str($val),",",str($val2),")"])
                        #else
                            #set c=''.join([str($op),"(",str($val),")"])
                        #end if
                        condition = $c
                    #else
                        #if $cond == 'dist' and $op == 'lt'
                            condition = abs(var(pos1) - var(pos2)) < $val
                        #elif $cond == 'dist' and $op == 'gt'
                            condition = abs(var(pos1) - var(pos2)) > $val
                        #elif $op == 'lt'
                            condition = var($cond) < $val
                        #elif $op == 'gt'
                            condition = var($cond) > $val
                        #end if
                    #end if
                #end if
            #end for

            #for $action in $rule.actions:
                #set actiontype = $action.action.action_select
                #if $actiontype == 'color':
                    #if $action.action.dynamic.dynamic_select == "static":
                        #set actionval = $circosColor($action.action.dynamic.action_value)
                        $actiontype = $actionval
                    #else
                        #set x_fill_color = $action.action.dynamic.action_value
                        #set x_fill_color_count = int(str($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
                #elif $actiontype == 'z':
                    #if $action.action.dynamic.dynamic_select == "static":
                        #set actionval = $action.action.dynamic.action_value
                        $actiontype = $actionval
                    #else
                        #set x_min = 1000 if $action.action.dynamic.invert else 1
                        #set x_max = 1 if $action.action.dynamic.invert else 1000
                        $actiontype = eval(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
                    $actiontype = $actionval
                #end if
            #end for

            $rule.continue_flow

        </rule>
    #end for
    </rules>
</link>
#end for
    ]]></configfile>
  </xml>

  <xml name="configfile_plot_highlight_conf">
    <configfile name="plot_highlight_conf"><![CDATA[
###for $hi, $highlight in enumerate($sec_heat.highlights):
##    #if $highlight.type_select == "plot_highlights":
##<plot>
##    type = highlight
##    file = data/highlight-${hi}.txt
##    r1   = ${highlight.r1}r
##    r0   = ${highlight.r0}r
##    color = ${highlight.fill_color}
##</plot>
##    #end if
###end for
    ]]></configfile>
  </xml>
  <xml name="configfile_highlight_conf">
    <configfile name="highlight_conf"><![CDATA[
##<highlights>
###for $hi, $highlight in enumerate($sec_heat.highlights):
##    #if $highlight.type_select == "normal":
##    <highlight>
##        file = data/highlight-${hi}.txt
##        r1   = ${highlight.r1}r
##        r0   = ${highlight.r0}r
##        color = ${highlight.fill_color}
##    </highlight>
##    #end if
###end for
##</highlights>
    ]]></configfile>
  </xml>
  <xml name="test_case">
    <configfile name="test_case_conf"><![CDATA[
<!--
mkdir -p test-data/my-test-case/;
#if $reference_genome.reference_genome_source == 'history':
    cp ${genome_fasta} test-data/my-test-case/input.fa;
#end if

#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):
cp ${file} test-data/my-test-case/${idx}-${jdx}.${file.ext};
        #end for
#else
cp ${data.plot_format.data_source} test-data/my-test-case/${idx}.${data.plot_format.data_source.ext};
    #end if
#end for
cp "$output_png" test-data/my-test-case/output.png;
cp "$output_svg" test-data/my-test-case/output.svg;
-->
<test>
    <param name="reference_genome|reference_genome_source" value="${reference_genome.reference_genome_source}"/>
    <param name="reference_genome|genome_fasta" value="my-test-case/input.fa" />
    <!-- ideograms -->
    <param name="ideogram|spacing" value="${ideogram.spacing}" />
    <param name="ideogram|radius" value="${ideogram.radius}" />
    <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 $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="${ticks.show_ticks}" />
    <param name="ticks|radius" value="${ticks.radius}" />
    <param name="ticks|color" value="${ticks.color}" />
    <param name="ticks|multiplier" value="${ticks.multiplier}" />
    #for $idx, $tick_group in enumerate($ticks.tick_group):
    <param name="ticks|tick_group_${idx}|tickspacing" value="${tick_group.spacing}" />
    <param name="ticks|tick_group_${idx}|size" value="${tick_group.size}" />
    <param name="ticks|tick_group_${idx}|show_tick_labels" value="${tick_group.show_tick_labels}" />
    <param name="ticks|tick_group_${idx}|label_size" value="${tick_group.label_size}" />
    <param name="ticks|tick_group_${idx}|label_offset" value="${tick_group.label_offset}" />
    <param name="ticks|tick_group_${idx}|label_format" value="${tick_group.format}" />
    #end for
    <!-- Data -->
    #for $idx, $data_group in enumerate($sec_tdd.data):
    <param name="sec_tdd|data_${idx}|r0" value="${data_group.r0}" />
    <param name="sec_tdd|data_${idx}|r1" value="${data_group.r1}" />
    <param name="sec_tdd|data_${idx}|orientation" value="${data_group.orientation}" />
    <param name="sec_tdd|data_${idx}|plot_format|plot_format_select" value="${data_group.plot_format.plot_format_select}" />
        <!-- Note, please double check your files -->
    #if str($data_group.plot_format.plot_format_select) == 'histogram':
        #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|extend_bins" value="${data_group.plot_format.format_specific.extend_bins}" />
    #else if str($data_group.plot_format.plot_format_select) == 'heatmap':
        #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|scale_log_base" value="${data_group.plot_format.format_specific.scale_log_base}" />
    #else if str($data_group.plot_format.plot_format_select) == 'line':
        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke" value="${data_group.plot_format.format_specific.stroke}" />
    #else if str($data_group.plot_format.plot_format_select) == 'scatter':
        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph" value="${data_group.plot_format.format_specific.glyph}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph_size" value="${data_group.plot_format.format_specific.glyph_size}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_min" value="${data_group.plot_format.format_specific.data_min}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_max" value="${data_group.plot_format.format_specific.data_max}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_color" value="${data_group.plot_format.format_specific.stroke_color}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
    #else if str($data_group.plot_format.plot_format_select) == 'tile':
        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|layers" value="${data_group.plot_format.format_specific.layers}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|thickness" value="${data_group.plot_format.format_specific.thickness}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|padding" value="${data_group.plot_format.format_specific.padding}" />
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|overflow_behavior" value="${data_group.plot_format.format_specific.overflow.overflow_behavior}" />
        #if str($data_group.plot_format.format_specific.overflow.overflow_behavior) != 'hide':
        <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|layer_overflow_color" value="${data_group.plot_format.format_specific.overflow.layer_overflow_color}" />
        #end if
    #end if
    ## Next line intentionally blank

    #end for


    <!-- Outputs -->
    <output name="output_png" file="my-test-case/output.png" />
    <output name="output_svg" file="my-test-case/output.svg" />
</test>
    ]]></configfile>
  </xml>
</macros>