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comparison circos.xml @ 7:4b519282a05b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
author iuc
date Mon, 25 May 2020 10:52:02 -0400
parents 740057a5126d
children df7356989ac1
comparison
equal deleted inserted replaced
6:740057a5126d 7:4b519282a05b
27 #if $reference_genome.ref.ref_source == 'history': 27 #if $reference_genome.ref.ref_source == 'history':
28 ln -s '$reference_genome.ref.genome_fasta' genomeref.fa && 28 ln -s '$reference_genome.ref.genome_fasta' genomeref.fa &&
29 #end if 29 #end if
30 30
31 #if $reference_genome.ref.ref_source in ('lengths', 'cached'): 31 #if $reference_genome.ref.ref_source in ('lengths', 'cached'):
32 python '$__tool_directory__/genome-lengths-to-karyotype.py' 32 python '$__tool_directory__/karyotype-from-lengths.py'
33 #if $reference_genome.ref.ref_source == 'lengths': 33 #if $reference_genome.ref.ref_source == 'lengths':
34 ${reference_genome.ref.input_lengths}' 34 ${reference_genome.ref.input_lengths}'
35 #else 35 #else
36 #if $ideogram.limit_chromosomes: 36 #if $ideogram.limit_chromosomes:
37 ## If they are limiting the chromosomes, ensure they have access to the full list 37 ## If they are limiting the chromosomes, ensure they have access to the full list
39 #else 39 #else
40 ## Otherwise only the reduced list, as the full list will often overwhelm circos 40 ## Otherwise only the reduced list, as the full list will often overwhelm circos
41 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}') 41 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}')
42 #end if 42 #end if
43 #end if 43 #end if
44 '${reference_genome.ref.color}'
45 > circos/conf/karyotype.txt && 44 > circos/conf/karyotype.txt &&
46 #else if $reference_genome.ref.ref_source == 'karyotype': 45 #else if $reference_genome.ref.ref_source == 'karyotype':
47 cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt && 46 cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt &&
48 #else if str($reference_genome.ref.ref_source) == 'history': 47 #else if str($reference_genome.ref.ref_source) == 'history':
49 ## Process the karyotype.txt file 48 ## Process the karyotype.txt file
50 python 49 python
51 '$__tool_directory__/fasta-to-karyotype.py' 50 '$__tool_directory__/karyotype-from-fasta.py'
52 genomeref.fa 51 genomeref.fa
53 '${reference_genome.ref.color}' 52 > circos/conf/karyotype.txt &&
54
55 > circos/conf/karyotype.txt &&
56 #else if $reference_genome.ref.ref_source == 'preset': 53 #else if $reference_genome.ref.ref_source == 'preset':
57 cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt && 54 cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt &&
58 #end if 55 #end if
56
57 python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'`
58 > 'circos/conf/karyotype-colors.conf' &&
59 59
60 touch circos/conf/karyotype-colors.conf && 60 touch circos/conf/karyotype-colors.conf &&
61 61
62 ## #if $ideogram.bands.bands: 62 ## #if $ideogram.bands.bands:
63 ## #if $ideogram.bands.convert_bands: 63 ## #if $ideogram.bands.convert_bands:
156 </when> 156 </when>
157 <when value="cached"> 157 <when value="cached">
158 <param name="fasta_indexes" type="select" label="Source Genome Build" help="Warning: this also contains unplaced scaffolds present in the reference genome. You can restrict the regions to plot in 'Limit/Filter Chromosomes' below, or supply your own file."> 158 <param name="fasta_indexes" type="select" label="Source Genome Build" help="Warning: this also contains unplaced scaffolds present in the reference genome. You can restrict the regions to plot in 'Limit/Filter Chromosomes' below, or supply your own file.">
159 <options from_data_table="__dbkeys__"/> 159 <options from_data_table="__dbkeys__"/>
160 </param> 160 </param>
161 <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/>
162 </when> 161 </when>
163 <when value="history"> 162 <when value="history">
164 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> 163 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
165 <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/>
166 </when> 164 </when>
167 <when value="karyotype"> 165 <when value="karyotype">
168 <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration" help="Provide your own karyotype configuration. Should be 'chr - ID LABEL START END COLOR'"/> 166 <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration" help="Provide your own karyotype configuration. Should be 'chr - ID LABEL START END COLOR'"/>
169 </when> 167 </when>
170 <when value="lengths"> 168 <when value="lengths">
171 <param name="input_lengths" type="data" format="tabular" label="Sequence Lengths" help="This needs to be a 2+ column tabular, e.g. from 'Compute sequence lengths', the first column should be chromosome and second should be length."/> 169 <param name="input_lengths" type="data" format="tabular" label="Sequence Lengths" help="This needs to be a 2+ column tabular, e.g. from 'Compute sequence lengths', the first column should be chromosome and second should be length."/>
172 <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/>
173 </when> 170 </when>
174 </conditional> 171 </conditional>
175 </section> 172 </section>
176 173
177 <section name="ideogram" title="Ideogram"> 174 <section name="ideogram" title="Ideogram">