Mercurial > repos > iuc > circos
diff macros.xml @ 2:014a21767ac4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
| author | iuc |
|---|---|
| date | Tue, 17 Sep 2019 16:54:57 -0400 |
| parents | ae9994cf526f |
| children | fd59d783248a |
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--- a/macros.xml Thu Oct 04 06:05:31 2018 -0400 +++ b/macros.xml Tue Sep 17 16:54:57 2019 -0400 @@ -1,21 +1,69 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">0.9-RC2</token> + <token name="@CIRCOS_VERSION@">0.69.8</token> + + <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy1</token> + <xml name="requirements"> <requirements> - <requirement type="package" version="0.69.5">circos</requirement> + <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="0.6.4">bcbiogff</requirement> <requirement type="package" version="1.70">biopython</requirement> + <requirement type="package" version="0.3.13">pybigwig</requirement> + <requirement type="package" version="0.23">circos-tools</requirement> + <yield /> </requirements> </xml> + <token name="@UTILS@"> +#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, $b +#end def +#def circosColorAlpha($value, $alpha) + #set $value = str($value) + #set $r = int($value[1:3], 16) + #set $g = int($value[3:5], 16) + #set $b = int($value[5:], 16) + #set $a = float($alpha) +$r, $g, $b, $a +#end def +#def chromosomesToOrder($value) + #set $q = ','.join([x if ':' not in x else x[x:x.index(':')] for x in str($value).split(';')]) + $q +#end def + </token> + <xml name="citations"> <citations> <citation type="doi">10.1101/gr.092759.109</citation> </citations> </xml> + <xml name="stroke_opts"> + <expand macro="circos_color_alpha" name="stroke_color" value="#000000" label="Stroke Color"/> + <param name="stroke_thickness" type="integer" value="1" label="Stroke Thickness"/> + </xml> + + <xml name="minmax"> + <conditional name="minmax"> + <param name="minmax_select" type="select" label="Minimum / maximum options"> + <option value="yes">Supply min/max values</option> + <option value="no" selected="true">Plot all values</option> + </param> + <when value="yes"> + <param name="min_value" type="float" value="1.0" label="Minimum value" /> + <param name="max_value" type="float" value="5.0" label="Maximum value" /> + </when> + <when value="no"> + </when> + </conditional> + </xml> + <xml name="circos_color" token_label="Color" token_name="color" @@ -31,26 +79,20 @@ </param> </xml> - <xml name="auto_color" + <xml name="circos_color_alpha" + token_label="Color" token_name="color" - token_label="Color"> - <conditional name="@NAME@" label="@LABEL@"> - <param name="@NAME@_select" type="select" label="@LABEL@"> - <option value="automatic" selected="true">Automatic Selection</option> - <option value="manual">Manual Specification</option> - </param> - <when value="automatic"> - </when> - <when value="manual"> - <param name="@NAME@" label="@LABEL@" type="color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#" /> - </valid> - </sanitizer> - </param> - </when> - </conditional> + token_value="#000000" + token_help="" + > + <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#" /> + </valid> + </sanitizer> + </param> + <param name="@NAME@_alpha" type="float" label="Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/> </xml> <xml name="brewer_scale" @@ -89,7 +131,7 @@ <option value="accent-8-qual">Qualitative: Accent</option> <option value="dark2-8-qual">Qualitative: Dark2</option> - <option value="paired-12-qual">Qualitative: Paired</option> + <option value="paired-12-qual" selected="true">Qualitative: Paired</option> <option value="pastel1-9-qual">Qualitative: Pastel1</option> <option value="pastel2-8-qual">Qualitative: Pastel2</option> <option value="set1-9-qual">Qualitative: Set1</option> @@ -98,11 +140,26 @@ </param> </xml> + <xml name="font_select" + token_normal="true" + token_bold="false"> + <param name="font" type="select" label="Font"> + <option value="light">light</option> + <option value="normal" selected="@NORMAL@">normal</option> + <option value="default">default</option> + <option value="semibold">semibold</option> + <option value="bold" selected="@BOLD@">bold</option> + <option value="italic">italic</option> + <option value="bolditalic">bolditalic</option> + <option value="italicbold">italicbold</option> + </param> + </xml> + <xml name="axes"> <section name="sec_axes" title="Axes"> <repeat name="axes" title="Axis"> - <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/> - <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/> + <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> + <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> <expand macro="circos_color"/> <param name="thickness" type="integer" value="1" label="Thickness"/> @@ -114,8 +171,8 @@ <xml name="backgrounds"> <section name="sec_bkgs" title="Backgrounds"> <repeat name="backgrounds" title="Background"> - <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/> - <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/> + <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> + <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> <expand macro="circos_color"/> </repeat> </section> @@ -130,8 +187,9 @@ <option value="1">Apply to Every Point</option> <option value="on">Check for presence/absence per chromosome</option> <option value="pos">Based on numerical position</option> + <option value="random">Randomly</option> <option value="value">Apply based on point value</option> - <option value="var">Apply based on GFF3 qualifier value (when available)</option> + <option value="var">Apply based on qualifier value (when available)</option> </param> <when value="1"> </when> @@ -139,20 +197,38 @@ <param name="on_genomes" type="text" label="Comma separated list of contig IDs"/> </when> <when value="pos"> - <param name="pos_gt" type="float" label="Greater than this base" value="1000.0" help="Leave as zero to disable this test"/> - <param name="pos_lt" type="float" label="Less than this base" value="0.0" help="Leave as zero to disable this test"/> + <param name="pos_gt" type="float" label="Greater than this base" optional="true"/> + <param name="pos_lt" type="float" label="Less than this base" optional="true"/> + <param name="pos_lt_sub" type="boolean" truevalue="yes" falsevalue="no" label="Count 'Less than this base' from end of chromosome" /> + </when> + <when value="random"> + <param name="value" type="float" label="Percentage of bins" value="0.5" min="0" max="1" help="Randomly apply with this probability"/> </when> <when value="value"> - <param name="pos_gt" type="float" label="Points above this value" value="0.0" help="Leave as zero to disable this test"/> - <param name="pos_lt" type="float" label="Points below this value" value="0.0" help="Leave as zero to disable this test"/> + <param name="pos_gt" type="float" label="Points above this value" optional="true"/> + <param name="pos_lt" type="float" label="Points below this value" optional="true"/> </when> <when value="var"> <param name="varname" type="text" label="Qualifier name" - help="Set to the name of the qualifier in the GFF3 file you wish to compare against" /> + help="Set to the name of the qualifier in the file you wish to compare against" /> <param name="cond_select" type="select" label="Condition"> <option value="eq">Equal to (string)</option> + <option value="==">Equal to (numeric)</option> <option value="ne">Not equal to (string)</option> + <option value="!=">Not equal to (numeric)</option> + <option value="<">Less than (numeric)</option> + <option value=">">Greater than (numeric)</option> + <option value="%">Modulus (numeric)</option> + <sanitizer> + <valid initial="string.letters"> + <add value=">" /> + <add value="<" /> + <add value="!" /> + <add value="=" /> + <add value="%" /> + </valid> + </sanitizer> </param> <param name="varvalue" type="text" label="Qualifier value to compare against"/> @@ -165,7 +241,7 @@ <option value="show">Change Visibility</option> <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="stroke_color">Change Stroke Color</option> <option value="color_value">Change Stroke Color based on Value</option> </param> <when value="show"> @@ -174,7 +250,7 @@ <when value="fill_color"> <expand macro="circos_color" name="action_value" label="Fill Color"/> </when> - <when value="color"> + <when value="stroke_color"> <expand macro="circos_color" name="action_value" label="Stroke Color"/> </when> <when value="fill_color_value"> @@ -203,7 +279,8 @@ <repeat name="conditions" title="Conditions to Apply" help="Multiple conditions will be combined using AND"> <conditional name="application"> <param name="application_select" type="select" label="Condition"> - <option value="always">True / Always Applied</option> + <option value="always" selected="true">True / Always Applied</option> + <option value="random">Randomly</option> <option value="interchr">Interchromosomal</option> <option value="intrachr">Intrachromosomal</option> <option value="chr">Chromosome</option> @@ -256,6 +333,9 @@ <when value="interchr"/> <when value="intrachr"/> <when value="always"/> + <when value="random"> + <param name="value" type="float" label="Percentage" value="0.5" min="0" max="1" help="Randomly apply with this probability"/> + </when> </conditional> </repeat> <repeat name="actions" title="Actions to Apply"> @@ -276,7 +356,7 @@ <option value="dynamic">Dynamic: Change is sometimes applied</option> </param> <when value="static"> - <expand macro="circos_color" label="Link Color" name="action_value"/> + <expand macro="circos_color_alpha" label="Link Color" name="action_value"/> </when> <when value="dynamic"> <expand macro="brewer_scale" label="Fill Color" name="action_value"/> @@ -339,7 +419,7 @@ </param> <!-- TODO select chromosome from metadata/file column instead of text fields --> <when value="on"> - <param name="compval" value="chr1" type="text" label="Chromosome"/> + <param name="compval" value="chr1" type="text" label="Chromosome" help="Comma separated values are supported in this field"/> </when> <when value="from"> <param name="compval" value="chr1" type="text" label="Chromosome"/>