| Previous changeset 6:740057a5126d (2020-05-01) Next changeset 8:e6cbe3190642 (2020-06-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a" |
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modified:
circos.xml macros.xml stack-histogram.py test-data/0/out.png test-data/0/out.svg test-data/1/out.png test-data/1/out.svg test-data/tableviewer/1.png |
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added:
karyotype-colors.py karyotype-from-fasta.py karyotype-from-lengths.py test-data/2/many.fa test-data/2/out.colors |
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removed:
fasta-to-karyotype.py genome-lengths-to-karyotype.py |
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| diff -r 740057a5126d -r 4b519282a05b circos.xml --- a/circos.xml Fri May 01 07:28:50 2020 -0400 +++ b/circos.xml Mon May 25 10:52:02 2020 -0400 |
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| @@ -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> |
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| diff -r 740057a5126d -r 4b519282a05b fasta-to-karyotype.py --- a/fasta-to-karyotype.py Fri May 01 07:28:50 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -#!/usr/bin/env python -import sys - -from Bio import SeqIO - -# Process fasta data, extracting only headers -for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")): - sys.stdout.write( - "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format( - seq_id=seq.id, - idx=idx, - length=len(seq), - color=((idx + 1) % 12), - theme=sys.argv[2], - ) - ) |
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| diff -r 740057a5126d -r 4b519282a05b genome-lengths-to-karyotype.py --- a/genome-lengths-to-karyotype.py Fri May 01 07:28:50 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -#!/usr/bin/env python -import csv -import sys - - -idx = 0 -with open(sys.argv[1], "r") as csvfile: - spamreader = csv.reader(csvfile, delimiter="\t", quotechar='"') - for row in spamreader: - if len(row) < 2: - continue - - seq_id = row[0] - length = row[1] - - sys.stdout.write( - "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format( - seq_id=seq_id, - idx=idx, - length=length, - color=((idx + 1) % 12), - theme=sys.argv[2], - ) - ) - idx += 1 |
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| diff -r 740057a5126d -r 4b519282a05b karyotype-colors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype-colors.py Mon May 25 10:52:02 2020 -0400 |
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| @@ -0,0 +1,11 @@ +#!/usr/bin/env python +import sys + + +highest = int(sys.argv[1]) +for idx in range(highest + 1): + sys.stdout.write( + "chr{idx}color = lch(66,104,{pos})\n".format( + idx=idx, pos=int(float(idx) / highest * 360) + ) + ) |
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| diff -r 740057a5126d -r 4b519282a05b karyotype-from-fasta.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype-from-fasta.py Mon May 25 10:52:02 2020 -0400 |
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| @@ -0,0 +1,12 @@ +#!/usr/bin/env python +import sys +from Bio import SeqIO + + +# Process fasta data, extracting only headers +for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")): + sys.stdout.write( + "chr - {seq_id} {seq_id} 0 {length} chr{idx}color\n".format( + seq_id=seq.id, idx=idx, length=len(seq) + ) + ) |
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| diff -r 740057a5126d -r 4b519282a05b karyotype-from-lengths.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype-from-lengths.py Mon May 25 10:52:02 2020 -0400 |
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| @@ -0,0 +1,23 @@ +#!/usr/bin/env python +import csv +import sys + + +idx = 0 +with open(sys.argv[1], "r") as csvfile: + spamreader = csv.reader(csvfile, delimiter="\t", quotechar='"') + for row in spamreader: + if len(row) < 2: + continue + + seq_id = row[0] + length = row[1] + + sys.stdout.write( + "chr - {seq_id} {seq_id} 0 {length} chr{idx}color\n".format( + seq_id=seq_id, + idx=idx, + length=length, + ) + ) + idx += 1 |
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| diff -r 740057a5126d -r 4b519282a05b macros.xml --- a/macros.xml Fri May 01 07:28:50 2020 -0400 +++ b/macros.xml Mon May 25 10:52:02 2020 -0400 |
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| @@ -2,7 +2,7 @@ <macros> <token name="@CIRCOS_VERSION@">0.69.8</token> - <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy5</token> + <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy6</token> <xml name="requirements"> <requirements> @@ -259,7 +259,7 @@ <option value="random">Randomly</option> <option value="on">Check for presence/absence per chromosome</option> <option value="pos">Based on position on chromosome</option> - <option value="value">Based on position value (ONLY for scatter/histogram/heatmap/line)</option> + <option value="value">Based on value (ONLY for scatter/histogram/heatmap/line)</option> <option value="var">Based on qualifier value (when available)</option> </param> <when value="always"> |
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| diff -r 740057a5126d -r 4b519282a05b stack-histogram.py --- a/stack-histogram.py Fri May 01 07:28:50 2020 -0400 +++ b/stack-histogram.py Mon May 25 10:52:02 2020 -0400 |
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| @@ -23,5 +23,5 @@ for chrom in k: for interval_set in zip(*[bw.intervals(chrom) for bw in bws]): (start, end) = interval_set[0][0:2] - values = ','.join(map(str, [x[2] for x in interval_set])) + values = ",".join(map(str, [x[2] for x in interval_set])) sys.stdout.write("%s\t%s\t%s\t%s\n" % (chrom, start, end, values)) |
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| diff -r 740057a5126d -r 4b519282a05b test-data/0/out.png |
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| Binary file test-data/0/out.png has changed |
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| diff -r 740057a5126d -r 4b519282a05b test-data/0/out.svg --- a/test-data/0/out.svg Fri May 01 07:28:50 2020 -0400 +++ b/test-data/0/out.svg Mon May 25 10:52:02 2020 -0400 |
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| diff -r 740057a5126d -r 4b519282a05b test-data/1/out.png |
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| Binary file test-data/1/out.png has changed |
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| diff -r 740057a5126d -r 4b519282a05b test-data/1/out.svg --- a/test-data/1/out.svg Fri May 01 07:28:50 2020 -0400 +++ b/test-data/1/out.svg Mon May 25 10:52:02 2020 -0400 |
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| b |
| diff -r 740057a5126d -r 4b519282a05b test-data/2/many.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2/many.fa Mon May 25 10:52:02 2020 -0400 |
| b |
| @@ -0,0 +1,52 @@ +>1 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>2 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>3 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>4 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>5 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>6 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>7 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>8 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>9 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>10 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>11 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>12 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>13 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>14 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>15 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>16 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>17 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>18 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>19 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>20 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>21 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>22 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>23 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>24 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>25 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca +>26 +actgtcggtacgtatcgtatcggtacgttgactgtacgtagctgaca |
| b |
| diff -r 740057a5126d -r 4b519282a05b test-data/2/out.colors --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2/out.colors Mon May 25 10:52:02 2020 -0400 |
| b |
| @@ -0,0 +1,26 @@ +chr0color = lch(50,121,0) +chr1color = lch(50,121,14) +chr2color = lch(50,121,28) +chr3color = lch(50,121,43) +chr4color = lch(50,121,57) +chr5color = lch(50,121,72) +chr6color = lch(50,121,86) +chr7color = lch(50,121,100) +chr8color = lch(50,121,115) +chr9color = lch(50,121,129) +chr10color = lch(50,121,144) +chr11color = lch(50,121,158) +chr12color = lch(50,121,172) +chr13color = lch(50,121,187) +chr14color = lch(50,121,201) +chr15color = lch(50,121,216) +chr16color = lch(50,121,230) +chr17color = lch(50,121,244) +chr18color = lch(50,121,259) +chr19color = lch(50,121,273) +chr20color = lch(50,121,288) +chr21color = lch(50,121,302) +chr22color = lch(50,121,316) +chr23color = lch(50,121,331) +chr24color = lch(50,121,345) +chr25color = lch(50,121,360) |
| b |
| diff -r 740057a5126d -r 4b519282a05b test-data/tableviewer/1.png |
| b |
| Binary file test-data/tableviewer/1.png has changed |
