circos: circgraph.xml annotate

annotate circgraph.xml @ 6:169adf243c0a draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec

author	eric-rasche
date	Sat, 10 Jun 2017 13:38:32 -0400
parents	b25b3518c2ce
children	eb3af6e9f633

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
6 169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	17 #if $reference_genome.reference_genome_source != 'karyotype':
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	18 ## Process the karyotype.txt file
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	19 python $__tool_directory__/fasta-to-karyotype.py
0 e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	20
6 169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	21 #if str($reference_genome.reference_genome_source) == 'cached':
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	22 "${reference_genome.fasta_indexes.fields.path}"
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	23 #else if str($reference_genome.reference_genome_source) == 'history':
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	24 genomeref.fa
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	25 #end if
0 e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	26
6 169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	27 #if $ideogram.bands:
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	28 "${ideogram.bands}"
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	29 #end if
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	30 > circos/conf/karyotype.txt &&
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	31 #else
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	32 cp $reference_genome.input_karyotype circos/conf/karyotype.txt &&
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	33 #end if
0 e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	34
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	35 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	36 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	37 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	38 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	39 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	40 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	41 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	42 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	43
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	44 ## 2D Data Plots
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	45 #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	46 #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	47 python $__tool_directory__/unified-tiles.py
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	48 "${data.plot_format.data_source}" "${data.plot_format.data_source.ext}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	49 > circos/data/data-${hi}.txt &&
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	50 #else:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	51 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	52 $data.plot_format.plot_format_select
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	53 #if str($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	54 #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	55 "${file}" "${file.ext}"
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	56 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	57 #else:
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	58 "${data.plot_format.data_source}" "${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	59 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	60 > 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	61 #end if
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	62 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	63
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	64 ## Link Tracks
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	65 #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	66 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	67 #end for
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	68
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	69 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	70
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	71 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	72 ]]></command>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	73 <configfiles>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	74 <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	75 <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	76 <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	77 <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	78 <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	79 <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	80 <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	81 <expand macro="test_case" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	82 </configfiles>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	83 <inputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	84 <conditional name="reference_genome">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	85 <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	86 <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	87 <option value="cached">Locally Cached</option>
6 169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	88 <option value="karyotype">Karyotype</option>
0 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 value="cached">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	91 <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	92 <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	93 </param>
6 169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	94 <!-- TODO: multiple band files? -->
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	95 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	96 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
0 e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	97 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	98 <when value="history">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	99 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
6 169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	100 <!-- TODO: multiple band files? -->
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	101 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	102 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	103 </when>
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	104 <when value="karyotype">
169adf243c0a planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec eric-rasche parents: 5 diff changeset	105 <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration"/>
0 e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	106 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	107 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	108
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	109 <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	110 <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	111 <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	112 <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	113
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	114 <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	115 <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	116 <!--<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	117 <!--<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	118 <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	119 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	120 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	121 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	122
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	123 <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	124 <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	125 <!--<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	126 <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	127 <expand macro="circos_color"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	128 <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	129 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	130
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	131 <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	132 <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	133 <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	134 <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	135 <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	136 <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	137 <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	138 <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	139 <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	140 <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	141 <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	142 <sanitizer>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	143 <valid>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	144 <add value="%" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	145 </valid>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	146 </sanitizer>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	147 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	148 </repeat>
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 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	151
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	152 <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	153 <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	154 <!-- Positioning -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	155 <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	156 <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	157 <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	158 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	159
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	160 <conditional name="plot_format">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	161 <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	162 <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	163 <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	164 <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	165 <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	166 <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	167 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	168 <when value="histogram">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	169 <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	170 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	171 <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	172 <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	173 <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	174 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	175 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	176 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	177 <when value="heatmap">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	178 <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	179 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	180 <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	181 <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	182 <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	183 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	184 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	185 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	186 <when value="line">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	187 <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	188 <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	189 <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	190 <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	191 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	192 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	193 <when value="scatter">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	194 <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	195 <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	196 <!-- 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	197 <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	198 <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	199 <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	200 <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	201 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	202 <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	203 <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	204 <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	205
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="#555555" label="Color" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	207 <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	208 <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	209 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	210 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	211 <when value="tile">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	212 <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	213 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	214 <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	215 <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	216 <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	217 <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	218 <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	219 <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	220 <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	221
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	222 <conditional name="overflow">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	223 <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	224 <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	225 <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	226 <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	227 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	228 <when value="hide">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	229 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	230 <when value="grow">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	231 <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	232 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	233 <when value="collapse">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	234 <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	235 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	236 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	237 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	238 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	239 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	240
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	241 <expand macro="rules" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	242 <expand macro="axes" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	243 <expand macro="backgrounds" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	244 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	245 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	246 <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	247 <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	248 <!-- Positioning -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	249 <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	250 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	251 <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	252 <conditional name="linktype">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	253 <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	254 <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	255 <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	256 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	257 <when value="yes">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	258 <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	259 <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	260 <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	261 <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	262 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	263 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	264 <when value="no"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	265 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	266 <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	267 <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	268 <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	269 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	270
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	271 <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	272 <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	273 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	274 <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	275 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	276 <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	277 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	278 <conditional name="perturbation">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	279 <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	280 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	281 <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	282 <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	283 </param>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	284 <when value="yes">
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	285 <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	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 <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	288 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	289 <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	290 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	291 <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	292 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	293 <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	294 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	295 <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	296 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	297 </when>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	298 <when value="no"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	299 </conditional>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	300 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	301 <expand macro="linkrules"/>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	302 </repeat>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	303 </section>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	304 </inputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	305 <outputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	306 <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	307 <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	308 <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	309 </outputs>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	310 <tests>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	311 <test>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	312 <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	313 <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	314 <!-- ideograms -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	315 <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	316 <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	317 <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	318 <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	319 <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	320 <!-- Ticks -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <!-- Data -->
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_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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345
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\|r0" value="0.7" />
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\|r1" value="0.79" />
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\|orientation" value="out" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359
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\|r0" value="0.6" />
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\|r1" value="0.69" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <!-- Links -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	373 <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	374 <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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	384 <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	385 <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	386 <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	387 <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	388 <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	389
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	390 <!-- Outputs -->
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	391 <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	392 <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	393 </test>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	394 </tests>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	395 <help><![CDATA[
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	396 Circos
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	397 ======
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	398
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	399 ]]></help>
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	400 <expand macro="citations" />
e8475d0195fe planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 358dd35a2150af4183d9303af1df4f63be0737cd eric-rasche parents: diff changeset	401 </tool>

Mercurial > repos > eric-rasche > circos

annotate circgraph.xml @ 6:169adf243c0a draft