Mercurial > repos > iuc > circos
diff circos.xml @ 7:4b519282a05b draft
"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 |
line wrap: on
line diff
--- a/circos.xml Fri May 01 07:28:50 2020 -0400 +++ b/circos.xml Mon May 25 10:52:02 2020 -0400 @@ -29,7 +29,7 @@ #end if #if $reference_genome.ref.ref_source in ('lengths', 'cached'): - python '$__tool_directory__/genome-lengths-to-karyotype.py' + python '$__tool_directory__/karyotype-from-lengths.py' #if $reference_genome.ref.ref_source == 'lengths': ${reference_genome.ref.input_lengths}' #else @@ -41,22 +41,22 @@ <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}') #end if #end if - '${reference_genome.ref.color}' > circos/conf/karyotype.txt && #else if $reference_genome.ref.ref_source == 'karyotype': cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt && #else if str($reference_genome.ref.ref_source) == 'history': ## Process the karyotype.txt file python - '$__tool_directory__/fasta-to-karyotype.py' + '$__tool_directory__/karyotype-from-fasta.py' genomeref.fa - '${reference_genome.ref.color}' - - > circos/conf/karyotype.txt && + > circos/conf/karyotype.txt && #else if $reference_genome.ref.ref_source == 'preset': cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt && #end if +python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'` + > 'circos/conf/karyotype-colors.conf' && + touch circos/conf/karyotype-colors.conf && ## #if $ideogram.bands.bands: @@ -158,18 +158,15 @@ <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."> <options from_data_table="__dbkeys__"/> </param> - <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/> </when> <when value="history"> <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> - <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/> </when> <when value="karyotype"> <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'"/> </when> <when value="lengths"> <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."/> - <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/> </when> </conditional> </section>