Mercurial > repos > eric-rasche > circos

comparison circgraph.xml @ 6:169adf243c0a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
5:b25b3518c2ce 6:169adf243c0a
12 12
13 #if $reference_genome.reference_genome_source == 'history': 13 #if $reference_genome.reference_genome_source == 'history':
14 ln -s $reference_genome.genome_fasta genomeref.fa; 14 ln -s $reference_genome.genome_fasta genomeref.fa;
15 #end if 15 #end if
16 16
17 ## Process the karyotype.txt file 17 #if $reference_genome.reference_genome_source != 'karyotype':
18 python $__tool_directory__/fasta-to-karyotype.py 18 ## Process the karyotype.txt file
19 19 python $__tool_directory__/fasta-to-karyotype.py
20 #if str($reference_genome.reference_genome_source) == 'cached': 20
21 "${reference_genome.fasta_indexes.fields.path}" 21 #if str($reference_genome.reference_genome_source) == 'cached':
22 #else if str($reference_genome.reference_genome_source) == 'history': 22 "${reference_genome.fasta_indexes.fields.path}"
23 genomeref.fa 23 #else if str($reference_genome.reference_genome_source) == 'history':
24 #end if 24 genomeref.fa
25 25 #end if
26 #if $ideogram.bands: 26
27 "${ideogram.bands}" 27 #if $ideogram.bands:
28 #end if 28 "${ideogram.bands}"
29 29 #end if
30 > circos/conf/karyotype.txt && 30 > circos/conf/karyotype.txt &&
31 #else
32 cp $reference_genome.input_karyotype circos/conf/karyotype.txt &&
33 #end if
31 34
32 mv $circos_conf circos/conf/circos.conf && 35 mv $circos_conf circos/conf/circos.conf &&
33 mv $ticks_conf circos/conf/ticks.conf && 36 mv $ticks_conf circos/conf/ticks.conf &&
34 mv $ideogram_conf circos/conf/ideogram.conf && 37 mv $ideogram_conf circos/conf/ideogram.conf &&
35 mv $data_conf circos/conf/2d.conf && 38 mv $data_conf circos/conf/2d.conf &&
80 <inputs> 83 <inputs>
81 <conditional name="reference_genome"> 84 <conditional name="reference_genome">
82 <param name="reference_genome_source" type="select" label="Reference Genome"> 85 <param name="reference_genome_source" type="select" label="Reference Genome">
83 <option value="history" selected="True">From History</option> 86 <option value="history" selected="True">From History</option>
84 <option value="cached">Locally Cached</option> 87 <option value="cached">Locally Cached</option>
88 <option value="karyotype">Karyotype</option>
85 </param> 89 </param>
86 <when value="cached"> 90 <when value="cached">
87 <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> 91 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
88 <options from_data_table="all_fasta"/> 92 <options from_data_table="all_fasta"/>
89 </param> 93 </param>
94 <!-- TODO: multiple band files? -->
95 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
96 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
90 </when> 97 </when>
91 <when value="history"> 98 <when value="history">
92 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> 99 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
100 <!-- TODO: multiple band files? -->
101 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
102 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
103 </when>
104 <when value="karyotype">
105 <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration"/>
93 </when> 106 </when>
94 </conditional> 107 </conditional>
95 108
96 <section name="ideogram" title="Ideogram Configuration (Genome/Chromosomes)"> 109 <section name="ideogram" title="Ideogram Configuration (Genome/Chromosomes)">
97 <param name="spacing" type="float" value="0.005" label="Spacing Between Ideograms"/> 110 <param name="spacing" type="float" value="0.005" label="Spacing Between Ideograms"/>
103 <!--<param type="float" value="0.95" label="Radius" name="radius"/>--> 116 <!--<param type="float" value="0.95" label="Radius" name="radius"/>-->
104 <!--<param type="float" value="10" label="Thickness" name="thickness"/>--> 117 <!--<param type="float" value="10" label="Thickness" name="thickness"/>-->
105 <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no" 118 <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no"
106 help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/> 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"/>
107 </section> 120 </section>
108 <!-- TODO: multiple band files? -->
109 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
110 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
111 </section> 121 </section>
112 122
113 <section name="ticks" title="Ticks"> 123 <section name="ticks" title="Ticks">
114 <param name="show_ticks" type="boolean" truevalue="yes" falsevalue="no" label="Show Ticks"/> 124 <param name="show_ticks" type="boolean" truevalue="yes" falsevalue="no" label="Show Ticks"/>
115 <!--<param type="boolean" label="Show Tick Labels" name="show_tick_labels" truevalue="true" falsevalue="false" />--> 125 <!--<param type="boolean" label="Show Tick Labels" name="show_tick_labels" truevalue="true" falsevalue="false" />-->