circos: circgraph.xml annotate

annotate circgraph.xml @ 5:b25b3518c2ce draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2

author	eric-rasche
date	Sat, 10 Jun 2017 12:55:28 -0400
parents	e8475d0195fe
children	169adf243c0a

rev	line source
0 e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	1 <?xml version="1.0"?>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	2 <tool id="circgraph" name="Circos Builder" version="@WRAPPER_VERSION@">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	3 <description>creates circos plots from standard bioinformatics datatypes.</description>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	4 <macros>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	5 <import>macros.xml</import>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	6 <import>macros_conffiles.xml</import>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	7 </macros>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	8 <expand macro="requirements"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	9 <command detect_errors="aggressive"><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	10 ## Directory structure
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	11 mkdir -p circos/conf/ circos/data/ &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	12
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	13 #if $reference_genome.reference_genome_source == 'history':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	14 ln -s $reference_genome.genome_fasta genomeref.fa;
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	15 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	16
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	17 ## Process the karyotype.txt file
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	18 python $__tool_directory__/fasta-to-karyotype.py
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	19
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	20 #if str($reference_genome.reference_genome_source) == 'cached':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	21 "${reference_genome.fasta_indexes.fields.path}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	22 #else if str($reference_genome.reference_genome_source) == 'history':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	23 genomeref.fa
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	24 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	25
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	26 #if $ideogram.bands:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	27 "${ideogram.bands}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	28 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	29
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	30 > circos/conf/karyotype.txt &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	31
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	32 mv $circos_conf circos/conf/circos.conf &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	33 mv $ticks_conf circos/conf/ticks.conf &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	34 mv $ideogram_conf circos/conf/ideogram.conf &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	35 mv $data_conf circos/conf/2d.conf &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	36 mv $links_conf circos/conf/links.conf &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	37 mv $plot_highlight_conf circos/conf/plot_highlight.conf &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	38 mv $highlight_conf circos/conf/highlight.conf &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	39 mv $test_case_conf circos/conf/galaxy_test_case.xml &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	40
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	41 ## 2D Data Plots
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	42 #for $hi, $data in enumerate($sec_tdd.data):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	43 #if str($data.plot_format.plot_format_select) == 'tile':
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	44 python $__tool_directory__/unified-tiles.py
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	45 "${data.plot_format.data_source}" "${data.plot_format.data_source.ext}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	46 > circos/data/data-${hi}.txt &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	47 #else:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	48 python $__tool_directory__/unified-histogram.py
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	49 $data.plot_format.plot_format_select
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	50 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	51 #for $fi, $file in enumerate($data.plot_format.data_source):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	52 "${file}" "${file.ext}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	53 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	54 #else:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	55 "${data.plot_format.data_source}" "${data.plot_format.data_source.ext}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	56 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	57 > circos/data/data-${hi}.txt &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	58 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	59 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	60
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	61 ## Link Tracks
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	62 #for $hi, $data in enumerate($sec_links.data):
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	63 cp "${data.data_source}" circos/data/links-${hi}.txt &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	64 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	65
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	66 tar cvfz circos.tar.gz circos &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	67
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	68 circos -conf circos/conf/circos.conf
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	69 ]]></command>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	70 <configfiles>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	71 <expand macro="configfile_circos_conf" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	72 <expand macro="configfile_ticks_conf" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	73 <expand macro="configfile_ideogram_conf" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	74 <expand macro="configfile_data_conf" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	75 <expand macro="configfile_links_conf" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	76 <expand macro="configfile_plot_highlight_conf" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	77 <expand macro="configfile_highlight_conf" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	78 <expand macro="test_case" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	79 </configfiles>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	80 <inputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	81 <conditional name="reference_genome">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	82 <param name="reference_genome_source" type="select" label="Reference Genome">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	83 <option value="history" selected="True">From History</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	84 <option value="cached">Locally Cached</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	85 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	86 <when value="cached">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	87 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	88 <options from_data_table="all_fasta"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	89 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	90 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	91 <when value="history">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	92 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	93 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	94 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	95
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	96 <section name="ideogram" title="Ideogram Configuration (Genome/Chromosomes)">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	97 <param name="spacing" type="float" value="0.005" label="Spacing Between Ideograms"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	98 <param name="radius" type="float" value="0.90" label="Radius"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	99 <param name="thickness" type="float" value="10" label="Thickness"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	100
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	101 <section name="ideogram_labels" title="Labels">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	102 <param name="show_label" type="boolean" truevalue="yes" falsevalue="no" label="Show Label"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	103 <!--<param type="float" value="0.95" label="Radius" name="radius"/>-->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	104 <!--<param type="float" value="10" label="Thickness" name="thickness"/>-->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	105 <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	106 help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	107 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	108 <!-- TODO: multiple band files? -->
5 b25b3518c2ce planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7561690774be81155d79a3c38a77c098c59aa9a2 eric-rasche parents: 0 diff changeset	109 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
0 e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	110 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	111 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	112
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	113 <section name="ticks" title="Ticks">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	114 <param name="show_ticks" type="boolean" truevalue="yes" falsevalue="no" label="Show Ticks"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	115 <!--<param type="boolean" label="Show Tick Labels" name="show_tick_labels" truevalue="true" falsevalue="false" />-->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	116 <param name="radius" type="float" value="1.0" label="Radius"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	117 <expand macro="circos_color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	118 <param name="multiplier" type="float" value="1e-3" label="Multiplier"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	119 help="1e-3 means your tick spacing will be in kb (tick spacing of 5000 = every 5kb, labels will read '5kb'). 1e-6 means mb."/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	120
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	121 <repeat name="tick_group" title="Tick Group">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	122 <param name="spacing" type="float" value="5000" label="Tick Spacing" help="Number of bases"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	123 <param name="size" type="float" value="10" label="Tick Size"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	124 <param name="show_tick_labels" type="boolean" truevalue="yes" falsevalue="no" label="Show Tick Labels"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	125 <param name="label_size" type="float" value="20" label="Label Size"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	126 <param name="label_offset" type="float" value="10" label="Label Offset"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	127 <param name="format" type="select" label="Label Format">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	128 <option value="%d" selected="True">Integer</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	129 <option value="%f">Float</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	130 <option value="%.1f">Float (one decimal)</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	131 <option value="%.2f">Float (two decimals)</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	132 <sanitizer>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	133 <valid>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	134 <add value="%" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	135 </valid>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	136 </sanitizer>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	137 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	138 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	139
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	140 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	141
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	142 <section name="sec_tdd" title="2D Data">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	143 <repeat name="data" title="2D Data Plot">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	144 <!-- Positioning -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	145 <param name="r1" type="float" value="0.89" label="Outside Radius"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	146 <param name="r0" type="float" value="0.8" label="Inside Radius"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	147 <param name="orientation" type="boolean" label="Orient Inwards" truevalue="in" falsevalue="out"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	148 help="When yes/true, the plot will face inwards. I.e. lowest values will be to the outside"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	149
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	150 <conditional name="plot_format">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	151 <param name="plot_format_select" type="select" label="Plot Format">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	152 <option value="histogram" selected="True">Histogram</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	153 <option value="heatmap">Heatmap</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	154 <option value="line">Line</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	155 <option value="scatter">Scatter</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	156 <option value="tile">Tiles</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	157 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	158 <when value="histogram">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	159 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Histogram Data Source"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	160 multiple="True" help="If multiple files are selected, they will be treated as a stacked histogram"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	161 <section name="format_specific" title="Plot Format Specific Options">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	162 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	163 <param name="extend_bins" type="boolean" label="Join non-abutting Bins" truevalue="yes" falsevalue="no"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	164 help="Join histogram bins that do not touch (abut)" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	165 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	166 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	167 <when value="heatmap">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	168 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Heatmap Data Source"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	169 multiple="True" help="If multiple files are selected, they will be plotted alongside each other radially"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	170 <section name="format_specific" title="Plot Format Specific Options">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	171 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	172 <param name="scale_log_base" type="float" value="1.0" label="Scale Log Base"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	173 help="If scale_log_base<1, the dynamic range of color mapping of small values will be increased. If scale_log_base>1, then dynamic range of large values will be increased."/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	174 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	175 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	176 <when value="line">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	177 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Line Data Source"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	178 <section name="format_specific" title="Plot Format Specific Options">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	179 <expand macro="circos_color" label="Stroke Color" name="color" value="#000000"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	180 <param name="thickness" type="integer" value="0" label="Stroke Thickness"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	181 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	182 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	183 <when value="scatter">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	184 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Scatter Plot Data Source"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	185 <section name="format_specific" title="Plot Format Specific Options">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	186 <!-- glyph, glyph_size, min, max -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	187 <param name="glyph" type="select" label="Glyph">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	188 <option value="circle">Circle</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	189 <option value="triangle">Triangle</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	190 <option value="rectangle">Rectangle</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	191 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	192 <param name="glyph_size" type="integer" value="8" label="Glyph Size"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	193 <param name="data_min" type="float" value="0.0" label="Data Minimum" help="Minimum value of the range of the plot axis, data outside this range are clipped." />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	194 <param name="data_max" type="float" value="1.0" label="Data Maximum" help="Maximum value of the range of the plot axis, data outside this range are clipped." />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	195
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	196 <expand macro="circos_color" name="color" value="#555555" label="Color" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	197 <expand macro="circos_color" name="stroke_color" value="#000000" label="Stroke Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	198 <param name="stroke_thickness" type="integer" value="0" label="Stroke Thickness"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	199 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	200 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	201 <when value="tile">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	202 <param name="data_source" type="data" format="bed6,bed12,gff3" label="Tile Data Source"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	203 help="If your tile source features have scores in them, they will be used in colouration"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	204 <section name="format_specific" title="Plot Format Specific Options">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	205 <expand macro="brewer_scale" name="fill_color" label="Fill Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	206 <expand macro="circos_color" name="color" value="#000000" label="Stroke Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	207 <param name="stroke_thickness" type="integer" value="0" label="Stroke Thickness"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	208 <param name="layers" type="integer" value="15" label="Layers"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	209 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	210 <param name="padding" type="float" value="8" label="Padding" help="In pixels"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	211
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	212 <conditional name="overflow">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	213 <param name="overflow_behavior" type="select" label="Overflow Behavior">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	214 <option value="hide">Hide: overflow tiles are not drawn</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	215 <option value="grow">Grow: new layers are added as required</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	216 <option value="collapse">Collapse: overflow tiles are drawn on the first layer</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	217 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	218 <when value="hide">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	219 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	220 <when value="grow">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	221 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	222 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	223 <when value="collapse">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	224 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	225 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	226 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	227 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	228 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	229 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	230
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	231 <expand macro="rules" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	232 <expand macro="axes" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	233 <expand macro="backgrounds" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	234 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	235 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	236 <section name="sec_links" title="Link Tracks">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	237 <repeat name="data" title="Link Data">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	238 <!-- Positioning -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	239 <param name="radius" type="float" value="0.8" label="Inside Radius"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	240 help="This is the radial position of the termination of the link; for relative values, if radius smaller than 1 then it is defined in terms of the inner ideogram radius, otherwise it is defined in terms of the outer ideogram radius" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	241 <param name="data_source" type="data" format="txt" label="Link Data Source" help="Select file with link data. Format: chr1 start1 end1 chr2 start2 end2" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	242 <conditional name="linktype">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	243 <param name="ribbon" type="select" label="Link Type" help="">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	244 <option value="no" selected="true">basic</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	245 <option value="yes">ribbon</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	246 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	247 <when value="yes">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	248 <param name="twist" type="select" label="Twist Ribbon">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	249 <option value="" selected="true">auto</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	250 <option value="twist=yes">always</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	251 <option value="flat=yes">never</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	252 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	253 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	254 <when value="no"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	255 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	256 <expand macro="circos_color" name="color" value="#000000" label="Link Color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	257 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	258 <param name="bezier_radius" type="float" value="0.1" min="0" max="1" label="Bezier Radius"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	259 help="The radial position of the third control point (in addition to the two positions defined by the link coordinates) used to draw the Bezier curve; if this parameter is 0 then straight lines will be used"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	260
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	261 <section name="advanced" title="Advanced Settings">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	262 <param name="zdepth" type="float" value="" optional="true" label="Z-depth"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	263 help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple link tracks"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	264 <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	265 help="Two additional Bezier control points can be set by using the crest parameter. When defined, points p3 and p4 are added. These points lie at the same angular position as the start and end link termini and have the radial position. In the crest=0 extreme, p3 and p4 are at the same position as p0,p1. In this case, crest has no effect. When crest=1, p3,p4 are at the radial position of p2, the control point set by bezier_radius"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	266 <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	267 help="The bezier_radius_purity adjusts the position of p2 for each link. The p2 control point will move along the line formed by the original p2 location and the intersection of p0-p1 and the bisecting radius. When purity = 1, p2' = p2. When purity = 0, p2' = midpoint(p0,p1)"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	268 <conditional name="perturbation">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	269 <param name="perturb" type="select" label="Perturb links?"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	270 help="A set of parameters can be used to randomly adjust bezier_radius, bezier_radius_purity, and crest parameters to give the links a more disorganized, organic feel. By perturbing each link you can also show additional texture in the data among links which would have ordinarily overlapped. Each parameter's perturbation amount is defined as a pair of values - pmin,pmax. These are the minimum and maximum multipliers by which the value can be perturbed">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	271 <option value="no" selected="true">no</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	272 <option value="yes">yes</option>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	273 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	274 <when value="yes">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	275 <param name="perturb_crest_min" type="float" value="0.5" label="Crest min"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	276 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	277 <param name="perturb_crest_max" type="float" value="1.5" label="Crest max"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	278 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	279 <param name="perturb_bezier_radius_min" type="float" value="0.5" label="Bezier Radius min"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	280 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	281 <param name="perturb_bezier_radius_max" type="float" value="1.5" label="Bezier Radius max"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	282 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	283 <param name="perturb_bezier_radius_purity_min" type="float" value="0.5" label="Bezier Radius Purity min"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	284 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	285 <param name="perturb_bezier_radius_purity_max" type="float" value="1.5" label="Bezier Radius Purity max"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	286 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	287 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	288 <when value="no"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	289 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	290 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	291 <expand macro="linkrules"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	292 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	293 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	294 </inputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	295 <outputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	296 <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot (png)"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	297 <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot (svg)"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	298 <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	299 </outputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	300 <tests>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	301 <test>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	302 <param name="reference_genome\|reference_genome_source" value="history"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	303 <param name="reference_genome\|genome_fasta" value="1/input.fa" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	304 <!-- ideograms -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	305 <param name="ideogram\|spacing" value="0.005" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	306 <param name="ideogram\|radius" value="0.9" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	307 <param name="ideogram\|thickness" value="10.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	308 <param name="ideogram\|ideogram_labels\|show_label" value="yes" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	309 <param name="ideogram\|ideogram_labels\|parallel" value="no" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	310 <!-- Ticks -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	311 <param name="ticks\|show_ticks" value="yes" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	312 <param name="ticks\|radius" value="1.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	313 <param name="ticks\|color" value="#17365d" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	314 <param name="ticks\|multiplier" value="0.001" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	315 <param name="ticks\|tick_group_0\|tickspacing" value="5000.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	316 <param name="ticks\|tick_group_0\|size" value="20.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	317 <param name="ticks\|tick_group_0\|show_tick_labels" value="yes" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	318 <param name="ticks\|tick_group_0\|label_size" value="20.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	319 <param name="ticks\|tick_group_0\|label_offset" value="10.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	320 <param name="ticks\|tick_group_0\|label_format" value="%d" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	321 <param name="ticks\|tick_group_1\|tickspacing" value="500.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	322 <param name="ticks\|tick_group_1\|size" value="10.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	323 <param name="ticks\|tick_group_1\|show_tick_labels" value="no" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	324 <param name="ticks\|tick_group_1\|label_size" value="20.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	325 <param name="ticks\|tick_group_1\|label_offset" value="10.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	326 <param name="ticks\|tick_group_1\|label_format" value="%d" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	327 <!-- Data -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	328 <param name="sec_tdd\|data_0\|r0" value="0.8" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	329 <param name="sec_tdd\|data_0\|r1" value="0.89" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	330 <param name="sec_tdd\|data_0\|orientation" value="out" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	331 <param name="sec_tdd\|data_0\|plot_format\|plot_format_select" value="histogram" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	332 <param name="sec_tdd\|data_0\|plot_format\|data_source" value="1/0-0.wig" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	333 <param name="sec_tdd\|data_0\|plot_format\|format_specific\|fill_color" value="purples-13-seq" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	334 <param name="sec_tdd\|data_0\|plot_format\|format_specific\|extend_bins" value="no" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	335
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	336 <param name="sec_tdd\|data_1\|r0" value="0.7" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	337 <param name="sec_tdd\|data_1\|r1" value="0.79" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	338 <param name="sec_tdd\|data_1\|orientation" value="out" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	339 <param name="sec_tdd\|data_1\|plot_format\|plot_format_select" value="tile" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	340 <param name="sec_tdd\|data_1\|plot_format\|data_source" value="1/1.gff3" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	341 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|fill_color" value="rdylgn-15-div" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	342 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|color" value="#000000" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	343 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|stroke_thickness" value="1" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	344 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|layers" value="15" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	345 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|thickness" value="15.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	346 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|padding" value="8.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	347 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|overflow\|overflow_behavior" value="grow" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	348 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|overflow\|layer_overflow_color" value="#ffc000" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	349
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	350 <param name="sec_tdd\|data_2\|r0" value="0.6" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	351 <param name="sec_tdd\|data_2\|r1" value="0.69" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	352 <param name="sec_tdd\|data_2\|orientation" value="out" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	353 <param name="sec_tdd\|data_2\|plot_format\|plot_format_select" value="scatter" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	354 <param name="sec_tdd\|data_2\|plot_format\|data_source" value="1/2.wig" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	355 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|glyph" value="triangle" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	356 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|glyph_size" value="8" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	357 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|data_min" value="0.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	358 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|data_max" value="1.0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	359 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|color" value="#555555" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	360 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|stroke_color" value="#000000" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	361 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|stroke_thickness" value="0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	362 <!-- Links -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	363 <param name="sec_links\|data_0\|radius" value="0.59" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	364 <param name="sec_links\|data_0\|data_source" value="1/links.txt" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	365 <param name="sec_links\|data_0\|linktype\|ribbon" value="yes" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	366 <param name="sec_links\|data_0\|color" value="#9966ff" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	367 <param name="sec_links\|data_0\|bezier_radius" value="0.3" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	368 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|conditions_0\|application\|application_select" value="pos1" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	369 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|conditions_0\|application\|comparison\|compare" value="lt" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	370 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|conditions_0\|application\|comparison\|compval" value="25000" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	371 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|actions_0\|action\|action_select" value="color" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	372 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|actions_0\|action\|action_value" value="#ffcc00" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	373
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	374 <param name="sec_links\|data_1\|radius" value="0.45" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	375 <param name="sec_links\|data_1\|data_source" value="1/links2.txt" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	376 <param name="sec_links\|data_1\|linktype\|ribbon" value="yes" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	377 <param name="sec_links\|data_1\|color" value="#42aa42" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	378 <param name="sec_links\|data_1\|bezier_radius" value="0" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	379
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	380 <!-- Outputs -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	381 <output name="output_png" file="1/output.png" compare="sim_size" ftype="png" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	382 <output name="output_svg" file="1/output.svg" compare="sim_size" ftype="svg" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	383 </test>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	384 </tests>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	385 <help><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	386 Circos
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	387 ======
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	388
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	389 ]]></help>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	390 <expand macro="citations" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	391 </tool>

Mercurial > repos > eric-rasche > circos

annotate circgraph.xml @ 5:b25b3518c2ce draft