# HG changeset patch
# User iuc
# Date 1771327602 0
# Node ID f4e0a4ee7a8357ba6c649cbb73cd9b7bca5f8be6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_collate commit 096bd5549dc8cafde08e9d9b7f7bd90f2e870e5c
diff -r 000000000000 -r f4e0a4ee7a83 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Feb 17 11:26:42 2026 +0000
@@ -0,0 +1,246 @@
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+ samtools
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+ 1.22
+ 1
+ 24.0
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+ &2 &&
+ gzip -dc \$reffa > reference.fa &&
+ reffa="reference.fa" &&
+ samtools faidx \$reffa;
+ }
+ } &&
+ #end if
+ reffai=\$reffa.fai &&
+ #elif $addref_cond.addref_select == "cached":
+ ## in case of cached the absolute path is used which allows to read
+ ## a cram file without specifying the reference
+ reffa='${addref_cond.ref.fields.path}' &&
+ reffai=\$reffa.fai &&
+ #else
+ #set use_ref=False
+ #end if
+ ]]>
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+ @HELP@
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+ @HELP@
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+ ^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$
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+ 10.1093/gigascience/giab008
+ 10.1093/bioinformatics/btr076
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+ &1 | grep Version]]>
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diff -r 000000000000 -r f4e0a4ee7a83 samtools_collate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_collate.xml Tue Feb 17 11:26:42 2026 +0000
@@ -0,0 +1,81 @@
+
+ shuffle and group reads together by their names
+
+ macros.xml
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diff -r 000000000000 -r f4e0a4ee7a83 test-data/fast_collate.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fast_collate.sam Tue Feb 17 11:26:42 2026 +0000
@@ -0,0 +1,27 @@
+@HD VN:1.4 SO:coordinate
+@SQ SN:contig_000000000 LN:11391
+@SQ SN:contig_000000008 LN:29043
+entry1 163 contig_000000000 109 60 250M = 137 278 GATTGATATTTATTTATTATTTTATTATGTTTATTTCTTTATTTATTATCATTATTATTATTATTCTTATTATTGTTATATAAAAACATCGTAAACACAGTAAACGATAGTACTAATACTACTACTAATAAAGATAGATTTTTTTATATATATATATGTATGATCTTTTAACGTTACTTATTCAAATGCTATGTCATTTTGTAATATTTGTCATGGCAAGTATCAAACTGCTTCGGTTCTCATTGATTAG 1111>DD3DFFF3B333B3FBG3D3A33BG3D3F3333AFG3DF3D33B22D22222222D2B2A2ADE2AA2DAG222BD22D11//11//00B110ABB2FD1?>/>A2@2@2@F2@F21GB11FDDF21111111B2B11>/?1FB22>>>22>B2BG22B12B>F>11/0<0/2B2222B2@G11>22@22@G222201?1??11F1=11>111>1-....000=0000=00 NM:i:18 AS:i:164 XS:i:0 MQ:i:60 MC:Z:250M ms:i:6744
+entry11 227 contig_000000000 109 60 250M = 137 278 GATTGATATTTATTTATTATTTTATTATGTTTATTTCTTTATTTATTATCATTATTATTATTATTCTTATTATTGTTATATAAAAACATCGTAAACACAGTAAACGATAGTACTAATACTACTACTAATAAAGATAGATTTTTTTATATATATATATGTATGATCTTTTAACGTTACTTATTCAAATGCTATGTCATTTTGTAATATTTGTCATGGCAAGTATCAAACTGCTTCGGTTCTCATTGATTAG 1111>DD3DFFF3B333B3FBG3D3A33BG3D3F3333AFG3DF3D33B22D22222222D2B2A2ADE2AA2DAG222BD22D11//11//00B110ABB2FD1?>/>A2@2@2@F2@F21GB11FDDF21111111B2B11>/?1FB22>>>22>B2BG22B12B>F>11/0<0/2B2222B2@G11>22@22@G222201?1??11F1=11>111>1-....000=0000=00 NM:i:18 AS:i:164 XS:i:0 MQ:i:60 MC:Z:250M ms:i:6744
+entry2 163 contig_000000000 109 60 250M = 137 278 TATTGATATTTATTTATTATTTTATTATGTTTATTTATTTATTTATTATCATTATTATTATTATTATTATTATTGTTATATACAAACATAGTAAACACAGTAAACGATAGTAGTAATACTACTACTAATAAATATATATTTTTTTATATATATATATGTATGTTCTTTTAATGTTAATTTTTCAAATGCTTTGGCATTTTGTAACATTTGTCATGCCATGTATCAAACTGCCTGGGTTATCATTGATTAG BBBBB5F5DFFFGGGFGGGGGGHHHHHHHHHGHHGHHHHHHHHHHHHGGHHHHHHHEHHGHHGHHFHHHHHGHHHHHFHHHD5A33FBGBFHGGGFGGEGGGBGGAEGAEHH5GD5FEGFD5GGFGHFHE4GHGGHHHHHHHDEEA?FGHHGHGHFBEFFHEGHH4GGHHCFFFHHFHHHHHHBFHG1FFBFF01BGHHHFCFF@1GHHBGGFHFF1?1?FBGGF11FD110FG.11=<<1><111@@11F//0A>2HG>B>2B22222B2FFB2BB22>>2B22BFBEEFGHHG2FGBB22FFB2DB1100F/1FG@G1BHHFGGAGB1DB@22EB00GCEADB1AFHHHGD21BEDF1AF1FA11DAA221BD1AA/EF00FF1FF2EDEBGEA0B03AD3D33AB1A1GEFGEFB3DB31>>11> NM:i:7 AS:i:222 XS:i:19 MQ:i:60 MC:Z:250M ms:i:5687
+entry11 211 contig_000000000 137 60 250M = 109 -278 TTTTATTTATTTATTTATTATCATTATTATTATTATTATTATTATTGTTATATAAGAACCTAGTAAACACAGTAAACGATAGTAGTAATACTACTACTAATAAATTTATATTTTTTTATATATATATATGTATGTTCTTTTAATGTTAATTTTTCAAATGCTTTGGCATTTTGTAACATTTGTCATGCCAAGTATCACACTGCCTGGGTTATCATTGATTCGGTACTAGAGATAGTGTTTAAATAATACG ;0C0G;0C0:0FFGDD00D==00000D=00D1D=1DDDF>11=<<1><111@@11F//0A>2HG>B>2B22222B2FFB2BB22>>2B22BFBEEFGHHG2FGBB22FFB2DB1100F/1FG@G1BHHFGGAGB1DB@22EB00GCEADB1AFHHHGD21BEDF1AF1FA11DAA221BD1AA/EF00FF1FF2EDEBGEA0B03AD3D33AB1A1GEFGEFB3DB31>>11> NM:i:7 AS:i:222 XS:i:19 MQ:i:60 MC:Z:250M ms:i:5687
+entry2 83 contig_000000000 137 60 250M = 109 -278 GTTTATTTATTTATTTATTATCATTATTATTATTATTATTATTATTGTTATATAAAAACATAGTAAACACAGTAAACGATAGTAGTAATACTACTACTAATAAATATATATTTTTTTATATATATATATGTATGTTCTTTTAATGTTAATTTTTCAAATGCTTTGGCATTTTGTAACATTTGTCATGCCAAGTATCAAACTGCCTGGGTTATCATTGATTAGGTACTAGAGATAGTGTTTAAATAATAAG 0GHHHBD0DFGHHHG@FGGFGFBGGHFHGHHHHHFFF?FGHHGGGGFGEGGHHGGGGHGFGDGHGHHFHEGFHGFGFFHFFHHFHGHFHBFGGF? NM:i:0 AS:i:250 XS:i:0 MQ:i:60 MC:Z:250M ms:i:9562
+entry6 69 contig_000000000 304 0 * = 304 0 GCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAG BCCCBCBCFFDDGGGGGGGGGGGHGGHHHHHHGHHGGGHHHHHHHHHHHHGGHGGHGGGGGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHHGGGGGHHHGGGGGGDGGHHHHGHHGHHHGHHGGGGGGGHHGGGGGGGGGGAGGGGGGDGAGFGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBEFFFFFFFFFEFFFFFFEFFFFFF AS:i:0 XS:i:0 MQ:i:49 MC:Z:35M215S ms:i:9339
+entry6 137 contig_000000000 304 49 35M215S = 304 0 ATTTTGTAACATTTGTCATGCCAAGTATCAAACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCT ABBBBFFFFFFFGGGGGGGGGGHHHHHHHHGHGHHHHHHHGHHHGHGHHHHHHFGHHGHHHIHHHHHIHHHHHHHHHGHHHHHHHHGHGGGGGHGGGGGHHHHHHHGG1EGGGGGGFHGGHHHGHGGGGGGHHHHGGCGFHHGHHHHFHEHHHHHHHGGGHHGGGHGEGHGFHGCGCFHHHHHHHGGGGD?FFGA9EFFGCGG?AGGFGGGGGGFFFFFFFFFFFFFFFFFBFFEF?FEBBFED.ACFF0 NM:i:0 AS:i:35 XS:i:0 MC:Z:* ms:i:9398
+entry5 83 contig_000000000 422 60 250M = 304 -368 TGTGTGTGTGTGTGAGTTTGAAAGCAATAGACAGAGGGTAAGACTGTGTAATAGAGTGTAAGAGAGTGTCAGAGTGAGTGTGTAAATGGACGCCTATCATTTAGCATGGGTCAATCTAGTGAAAGCTCGCAGCAGCTCTCTAAGTGTCTGGCATTGCAGCAAATTGAGCCGAATGCATTTCTGCACACGTAAACACGGCAGAATACAGATTAGCCAAGCCCAATCTCTCATTAAATCCACATTTAATAGA .DDFGEAGGGFGFHGHHFFHHHHHHHHHHGCHHHHHHFFHHHHHHHHHHHHHHHHHHGHHFHHHHHHGHHHHHHHHHGHHHHHHHHGGGGGHGHHHFHHHHFHHHHHHHHHGHHHHHHHHHHHEEEEGHHHHHHHGHHHHHHHHHGHGHHHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHGHFHHHGGGHHHHHHHHHHHHHHGHHGGHHHHHHFHEFCHHGGGGGGGGGGFFFFFFFCCCCC NM:i:0 AS:i:250 XS:i:0 MQ:i:60 MC:Z:250M ms:i:9461
+entry7 121 contig_000000000 3891 60 250M = 3891 0 ACACCACCAGCACCAGCCTAAACCGTTGATACAAGGCAGGATGGATCCGTGCTTTCATGTTGTTGATGCTAAATTCTGACTCACATCTGAATATTCCAGCAGAAATCGAGACTCATCAGAGCAGGCAACGTTTTTACAATCTTTTATTGTCCAATTTTGGTGAGCCTGTGTGAATTGTAGTCTCAGTTTCCTGTTCTTAGCTGACAGGAGTGGCACCCGGTGTGGTCTTCTGCTGCTGTAGCCCATCCGC 99;GFC/0FC;/AFGFC0BDA.?BGFFC0FB9G0C/HHGBFHG:.GFCGEHGHGHFHHHEFHHGBGDF1EHF1GFGGFDFHFHHHFHHG1BG1HHGHHEHGBC>2<2HHHHFHHFHHHHFEGD2EFHHGEF4EHHFFG?/GGF3GFFCE3HGHFHGAHFGF1AGHHGGHHGD5HGF3HF3HHFHHHGHG1FEHHHFHHHEHHGFHHHFHHHHFGGCECEEGHHHGHHHGGGGFGGFFGFFF4BBBBBABB NM:i:0 AS:i:250 XS:i:0 MC:Z:* ms:i:4569
+entry7 181 contig_000000000 3891 0 * = 3891 0 CAGTCACTCGCCTCCCGCTAACAGTCCAACTCTTCTGGTTCATCTGCGAGTCATGGTGTACCGATGTTTTGTTCTCTAGAAAGCGAAAACATTGATATGGCTGAGGGGGGCTAGCAATTTTGGCCTGATAATGGGTGTGAAATATTCAAACTGTTATGATGCTAGCCCAAATAAAACTGTTGGGACTATCTCGGGAAGAAAAATCATGATCAGAGAAGCTAGGAAAGTGTCCTTGGTATGGTAAGCACTG ////-------;----0090;.9/0/000A//::.;.0000::.?@<=0/0=0./00..<..11>00>>0111?1@222B22@211122B11E@22112110000/B222A222ADB//0FB2DDBA///A/01D11011ADD211D1211BA11A311331D1A10B1FAFB1A1B3111@33111>11 AS:i:0 XS:i:0 MQ:i:60 MC:Z:250M ms:i:8580
+entry8 121 contig_000000000 3891 60 250M = 3891 0 ACACCACCAGCACCAGCCTAAACCGTTGATACAAGGCAGGATGGATCCGTGCTTTCATGTTGTTGATGCTAAATTCTGACTCACATCTGAATATTCCAGCAGAAATCGAGACTCATCAGAGCAGGCAACGTTTTTACAATCTTTTATTGTCCAATTTTGGTGAGCCTGTGTGAATTGTAGTCTCAGTTTCCTGTTCTTAGCTGACAGGAGTGGCACCCGGTGTGGTCTTCTGCTGCTGTAGCCCATCCGC 99;.9//FFF9/GFB9FBGBC.A.FCFGFGFBHHGB:0GHFCG-AA@CHGC0FFGGC.HC>>//2221122222@11>///CE?>/>//1112211111012B22222AD22110011111B/0A///B01111111ABB0013ED10FE1B111333A3333@33D>>1111 AS:i:0 XS:i:0 MQ:i:60 MC:Z:250M ms:i:8542
+entry9 163 contig_000000008 28855 12 54S189M7S = 28855 189 CAGTTGGGTTAAATATTTGGTGCTTTGTTGGGTTGTTTATAACCTTTATTTAGTTATTTATATTATAACTCAACCAGTTGGGTTAAATATTTGGTGCTTTGTTGGGTTGTTTATAACCTTTATGTAGTTATTTATATTATAACTCAACCAGTTGGGTTAAATATTTGGTGCTTTGTTGTGTTGTTTATAACCTTTATTTAGTTATTTATATTATAACTCAACCAGTTGGGTTAAATATTTGGTACTTTGT BCCBBFFCBCCFGGGGGGGGGGGHHHHHHHHGGGGGHHHHHHHHHHHHF5DGG5BGFDG5GFHFEHF5F553GHA1GEGHFEAFAF5FEGHFHFF1EGGHHHHHGCEFEEGFHFHFHFHHHH4444?44FE4B4?4D44D444433B20/??FH2?/?/32222D2FB//F>2FDHF00???/??CHGGGHFHBGHB<>1<<1DF1D0=<0FDGB0=000