# HG changeset patch
# User iuc
# Date 1771355348 0
# Node ID 61fa9655ab32c04f88ecd33e75ba80b6ec91be1a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromap commit 392fc1bebfff21996c13ba0edb952b5f3784cca2
diff -r 000000000000 -r 61fa9655ab32 chromap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chromap.xml Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,441 @@
+
+ Fast alignment and preprocessing of chromatin profiles
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+ macros.xml
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+ output_options['summary']
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diff -r 000000000000 -r 61fa9655ab32 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,21 @@
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+ 0.3.2
+ 0
+ 25.0
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+ chromap
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+ 10.1038/s41467-021-26865-w
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\ No newline at end of file
diff -r 000000000000 -r 61fa9655ab32 test-data/barcode.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barcode.fq Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,32 @@
+@read_1
+TAAACTTGGCTTGACT
++
+IIIIIIIIIIIIIIII
+@read_2
+TGAGCTCGCTTTAACG
++
+IIIIIIIIIIIIIIII
+@read_3
+TCGCTACACGCCGAAT
++
+IIIIIIIIIIIIIIII
+@read_4
+CATATATGACAATTCT
++
+IIIIIIIIIIIIIIII
+@read_5
+GCACGGGTAAAAAAGC
++
+IIIIIIIIIIIIIIII
+@read_6
+CCACAATGAATCTTTA
++
+IIIIIIIIIIIIIIII
+@read_7
+CCGTTTGGTCGACGAT
++
+IIIIIIIIIIIIIIII
+@read_8
+CATCTGCCCGCTCTGG
++
+IIIIIIIIIIIIIIII
diff -r 000000000000 -r 61fa9655ab32 test-data/read1.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/read1.fq Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,32 @@
+@read_1/1
+TAACGGAGATCGTGCGAATAACCTGTCTAATATCTACTAAAGGTATCTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_2/1
+CGTTAATTAAAGACCAAGAACTTGCAATTTGGCATTCAATTAACTCTACC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_3/1
+TGATCCAAACCCTACGGCGACAGCAAATAGGAGATCCATAAGGAGTTAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_4/1
+CTCACACAATGTGTTTAGACTGGGTAGTTCGTTTTAATCGCGTTAATTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_5/1
+CGTAAGGTGAAAATTAAGGATTTATCTGCGTATGCCTGTGAATATGTATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_6/1
+GGAGCGACGTTTTTCCACGCGTGCACTTTGACCACATGTACAAGTCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_7/1
+AACTCTAGAATTCAGGGATTTCCTGGGCAAGAAAATTAAGGTGCGGGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_8/1
+TCTTCGTTATGGGATCTGACGAATTACCTACTGTACCATTCTCCAGTCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 000000000000 -r 61fa9655ab32 test-data/read1_se.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/read1_se.fq Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,32 @@
+@read_1
+TAACGGAGATCGTGCGAATAACCTGTCTAATATCTACTAAAGGTATCTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_2
+CGTTAATTAAAGACCAAGAACTTGCAATTTGGCATTCAATTAACTCTACC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_3
+TGATCCAAACCCTACGGCGACAGCAAATAGGAGATCCATAAGGAGTTAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_4
+CTCACACAATGTGTTTAGACTGGGTAGTTCGTTTTAATCGCGTTAATTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_5
+CGTAAGGTGAAAATTAAGGATTTATCTGCGTATGCCTGTGAATATGTATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_6
+GGAGCGACGTTTTTCCACGCGTGCACTTTGACCACATGTACAAGTCGAAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_7
+AACTCTAGAATTCAGGGATTTCCTGGGCAAGAAAATTAAGGTGCGGGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_8
+TCTTCGTTATGGGATCTGACGAATTACCTACTGTACCATTCTCCAGTCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 000000000000 -r 61fa9655ab32 test-data/read2.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/read2.fq Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,32 @@
+@read_1/2
+GGTAGAGTTAATTGAATGCCAAATTGCAAGTTCTTGGTCTTTAATTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_2/2
+GTTAACTCCTTATGGATCTCCTATTTGCTGTCGCCGTAGGGTTTGGATCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_3/2
+ACAATTAACGCGATTAAAACGAACTACCCAGTCTAAACACATTGTGTGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_4/2
+TATACATATTCACAGGCATACGCAGATAAATCCTTAATTTTCACCTTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_5/2
+GTTCGACTTGTACATGTGGTCAAAGTGCACGCGTGGAAAAACGTCGCTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_6/2
+AAGCCCGCACCTTAATTTTCTTGCCCAGGAAATCCCTGAATTCTAGAGTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_7/2
+GAGACTGGAGAATGGTACAGTAGGTAATTCGTCAGATCCCATAACGAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@read_8/2
+AATAATGTACAAATCGGTTTATGTCGTTCAATATCTGCAGCTACGGCTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 000000000000 -r 61fa9655ab32 test-data/ref.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fa Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,18 @@
+>chr1
+GAAAGGCATAATAAGTATCACGTACTAACGCGTCTTCGCTGAAAAAAAGTTAACGGAGAT
+CGTGCGAATAACCTGTCTAATATCTACTAAAGGTATCTCCAGGTAGATTCCATACCAGGA
+GTGTATACCCTACCATAGGATTACTATGATCGTTAATTAAAGACCAAGAACTTGCAATTT
+GGCATTCAATTAACTCTACCCCCATATATCAGTTCCTGAACTTGATTCACAATGAACATG
+TTTCAGATGATGATCCAAACCCTACGGCGACAGCAAATAGGAGATCCATAAGGAGTTAAC
+CTCTAATCGCCAAAGCTGACCCCCAGTCCCCAGACCACTTGAAATCCAGTCTCACACAAT
+GTGTTTAGACTGGGTAGTTCGTTTTAATCGCGTTAATTGTTATCGAATGTCGGAAAATCA
+TGAGTAGAGGATACTAACTCGCTCCGGTCTCGTAAGGTGAAAATTAAGGATTTATCTGCG
+TATGCCTGTGAATATGTATAGATTAGATATATGTGCAAATCTGGGGCAAAAGTAGGAGGA
+CCAATGCTGAGGAGCGACGTTTTTCCACGCGTGCACTTTGACCACATGTACAAGTCGAAC
+AGTGGGTGAAGTTTTTGTGAAAAATGAATGCTAAAAAATACTGACTCTTTAACTCTAGAA
+TTCAGGGATTTCCTGGGCAAGAAAATTAAGGTGCGGGCTTGCCAATGTAAGGCTTAATTA
+ACCTCCGAAGTGCATGTATTGCTGACCTTTTCTTCGTTATGGGATCTGACGAATTACCTA
+CTGTACCATTCTCCAGTCTCAATCTATTTTTTAGTAGAGGCTGCCTATTCCTTTGTGATC
+TGGCCCTTGGCAAGCCGTAGCTGCAGATATTGAACGACATAAACCGATTTGTACATTATT
+CACGATGGAGTCAGGTGGGGGCGCGTTTGAAGAATCTCCACTCGTACACCGCCCTGATTG
+GTCCAAACTCAACCTTACTTACATGGCTGATATTCATTCC
diff -r 000000000000 -r 61fa9655ab32 test-data/test01_mapping.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test01_mapping.bed Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,8 @@
+chr1 50 200 N 60 + 1
+chr1 150 300 N 60 + 1
+chr1 250 400 N 60 + 1
+chr1 350 500 N 60 + 1
+chr1 450 600 N 60 + 1
+chr1 550 700 N 60 + 1
+chr1 650 800 N 60 + 1
+chr1 750 900 N 60 + 1
diff -r 000000000000 -r 61fa9655ab32 test-data/test01_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test01_summary.txt Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,2 @@
+barcode,total,duplicate,unmapped,lowmapq,cachehit,fric,estfrip,numcacheslots
+,8,0,0,0,0,0.00000,0.00000,0
diff -r 000000000000 -r 61fa9655ab32 test-data/test02_mapping.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test02_mapping.sam Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,9 @@
+@SQ SN:chr1 LN:1000
+read_1 0 chr1 51 60 50M * 0 0 TAACGGAGATCGTGCGAATAACCTGTCTAATATCTACTAAAGGTATCTCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
+read_2 0 chr1 151 60 50M * 0 0 CGTTAATTAAAGACCAAGAACTTGCAATTTGGCATTCAATTAACTCTACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
+read_3 0 chr1 251 60 50M * 0 0 TGATCCAAACCCTACGGCGACAGCAAATAGGAGATCCATAAGGAGTTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
+read_4 0 chr1 351 60 50M * 0 0 CTCACACAATGTGTTTAGACTGGGTAGTTCGTTTTAATCGCGTTAATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
+read_5 0 chr1 451 60 50M * 0 0 CGTAAGGTGAAAATTAAGGATTTATCTGCGTATGCCTGTGAATATGTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
+read_6 0 chr1 551 60 50M * 0 0 GGAGCGACGTTTTTCCACGCGTGCACTTTGACCACATGTACAAGTCGAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
+read_7 0 chr1 651 60 50M * 0 0 AACTCTAGAATTCAGGGATTTCCTGGGCAAGAAAATTAAGGTGCGGGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
+read_8 0 chr1 751 60 50M * 0 0 TCTTCGTTATGGGATCTGACGAATTACCTACTGTACCATTCTCCAGTCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:50
diff -r 000000000000 -r 61fa9655ab32 test-data/test03_mapping.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test03_mapping.tsv Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,16 @@
+chr1 50 100 N 39 +
+chr1 150 200 N 39 - 1
+chr1 150 200 N 39 +
+chr1 250 300 N 39 - 1
+chr1 250 300 N 39 +
+chr1 350 400 N 39 - 1
+chr1 350 400 N 39 +
+chr1 450 500 N 39 - 1
+chr1 450 500 N 39 +
+chr1 550 600 N 39 - 1
+chr1 550 600 N 39 +
+chr1 650 700 N 39 - 1
+chr1 650 700 N 39 +
+chr1 750 800 N 39 - 1
+chr1 750 800 N 39 +
+chr1 850 900 N 39 - 1
diff -r 000000000000 -r 61fa9655ab32 test-data/test04_mapping.pairs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test04_mapping.pairs Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,12 @@
+## pairs format v1.0.0
+#shape: upper triangle
+#chromsize: chr1 1000
+#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type
+read_1/1 chr1 51 chr1 200 + - UU
+read_2/1 chr1 151 chr1 300 + - UU
+read_3/1 chr1 251 chr1 400 + - UU
+read_4/1 chr1 351 chr1 500 + - UU
+read_5/1 chr1 451 chr1 600 + - UU
+read_6/1 chr1 551 chr1 700 + - UU
+read_7/1 chr1 651 chr1 800 + - UU
+read_8/1 chr1 751 chr1 900 + - UU
diff -r 000000000000 -r 61fa9655ab32 test-data/test05_mapping.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test05_mapping.bed Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,8 @@
+chr1 54 104 TAAACTTGGCTTGACT 1
+chr1 154 204 TGAGCTCGCTTTAACG 1
+chr1 254 304 TCGCTACACGCCGAAT 1
+chr1 354 404 CATATATGACAATTCT 1
+chr1 454 504 GCACGGGTAAAAAAGC 1
+chr1 554 604 CCACAATGAATCTTTA 1
+chr1 654 704 CCGTTTGGTCGACGAT 1
+chr1 754 804 CATCTGCCCGCTCTGG 1
diff -r 000000000000 -r 61fa9655ab32 test-data/test05_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test05_summary.txt Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,10 @@
+barcode,total,duplicate,unmapped,lowmapq,cachehit,fric,estfrip,numcacheslots
+TCGCTACACGCCGAAT,1,0,0,0,0,0.00000,0.00000,0
+CCGTTTGGTCGACGAT,1,0,0,0,0,0.00000,0.00000,0
+TGAGCTCGCTTTAACG,1,0,0,0,0,0.00000,0.00000,0
+CATATATGACAATTCT,1,0,0,0,0,0.00000,0.00000,0
+TAAACTTGGCTTGACT,1,0,0,0,0,0.00000,0.00000,0
+GCACGGGTAAAAAAGC,1,0,0,0,0,0.00000,0.00000,0
+CATCTGCCCGCTCTGG,1,0,0,0,0,0.00000,0.00000,0
+CCACAATGAATCTTTA,1,0,0,0,0,0.00000,0.00000,0
+non-whitelist,0,0,0,0,0,0.00000,0.00000,0
diff -r 000000000000 -r 61fa9655ab32 test-data/test06_mapping.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test06_mapping.bed Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,8 @@
+chr1 54 104 N 60 + 1
+chr1 154 204 N 60 + 1
+chr1 254 304 N 60 + 1
+chr1 354 404 N 60 + 1
+chr1 454 504 N 60 + 1
+chr1 554 604 N 60 + 1
+chr1 654 704 N 60 + 1
+chr1 754 804 N 60 + 1
diff -r 000000000000 -r 61fa9655ab32 test-data/whitelist.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/whitelist.txt Tue Feb 17 19:09:08 2026 +0000
@@ -0,0 +1,8 @@
+TAAACTTGGCTTGACT
+TGAGCTCGCTTTAACG
+TCGCTACACGCCGAAT
+CATATATGACAATTCT
+GCACGGGTAAAAAAGC
+CCACAATGAATCTTTA
+CCGTTTGGTCGACGAT
+CATCTGCCCGCTCTGG