# HG changeset patch
# User iuc
# Date 1590418322 14400
# Node ID 4b519282a05b61c8dcb4e466acf22da78775e0fc
# Parent 740057a5126d2d133aa4cec493189f9bbb1eb1c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
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
@@ -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 @@
-
-
-
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
@@ -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],
- )
- )
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
@@ -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
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
@@ -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)
+ )
+ )
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
@@ -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)
+ )
+ )
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
@@ -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
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
@@ -2,7 +2,7 @@
0.69.8
- @CIRCOS_VERSION@+galaxy5
+ @CIRCOS_VERSION@+galaxy6
@@ -259,7 +259,7 @@
-
+
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
@@ -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))
diff -r 740057a5126d -r 4b519282a05b test-data/0/out.png
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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
@@ -5,17 +5,17 @@
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+
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diff -r 740057a5126d -r 4b519282a05b test-data/1/out.png
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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
@@ -5,2788 +5,2788 @@
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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
@@ -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
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
@@ -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)
diff -r 740057a5126d -r 4b519282a05b test-data/tableviewer/1.png
Binary file test-data/tableviewer/1.png has changed