# HG changeset patch
# User iuc
# Date 1763364630 0
# Node ID 65edd5a6002e685208f47685dc13437b7ae9a94b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_consensus commit 8d2369dc1bdafc743920a155c508c20114ebe655
diff -r 000000000000 -r 65edd5a6002e macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Nov 17 07:30:30 2025 +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 65edd5a6002e macros_tool_specific.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_tool_specific.xml Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,65 @@
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\ No newline at end of file
diff -r 000000000000 -r 65edd5a6002e samtools_consensus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_consensus.xml Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,615 @@
+
+ generate consensus from a SAM, BAM or CRAM file
+
+ macros.xml
+ macros_tool_specific.xml
+
+ ## additional reference data
+ #if $use_ref:
+ -T "\$reffa"
+ #end if
+
+
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+ $output_file
+ ]]>
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\ No newline at end of file
diff -r 000000000000 -r 65edd5a6002e test-data/consen1c.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/consen1c.fa Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,8 @@
+>c1
+GAAAAAAAAG
+>c2
+GTCCAAGGTAACCTG
+>c3
+ATTCAAAAAAAACTTAGGGTCCCCCCCCTGA
+>c4
+TCCCCCCCCT
diff -r 000000000000 -r 65edd5a6002e test-data/consen1c.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/consen1c.sam Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,18 @@
+@SQ SN:c1 LN:10
+@SQ SN:c2 LN:15
+@SQ SN:c3 LN:31
+@SQ SN:c4 LN:10
+@CO c2 CC***AAGGTAA***CC
+@CO
+@CO +s1a CC***AAGG*AA***CC
+@CO +s1b CC***AAGG*AA***CC
+@CO +s2a CCTTTAAGG*AATTTCC
+@CO +s2b CCTTTAACG*AATTTCC
+@CO +s3 CCTTTAA***AATTTCC
+s1a 0 c2 3 0 6M1D4M * 0 0 CCAAGGAACC IIII&IIIII
+s1b 0 c2 3 0 6M1D4M * 0 0 CCAAGGAACC IIII&IIIII
+s2a 0 c2 3 0 2M3I4M1D2M3I2M * 0 0 CCTTTAAGGAATTTCC IIIIIII&IIIIIIII
+s2b 0 c2 3 0 2M3I4M1D2M3I2M * 0 0 CCTTTAACGAATTTCC IIIIIIIIIIIIIIII
+s3 0 c2 3 0 2M3I2M3D2M3I2M * 0 0 CCTTTAAAATTTCC IIIIII&&IIIIII
+s4 0 c3 4 0 10M * 0 0 GAAAAAAAAG AAAAAZZZZZ
+s5 0 c3 20 0 10M * 0 0 TCCCCACCCT AAAAAZZZZZ
diff -r 000000000000 -r 65edd5a6002e test-data/ex1.bam
Binary file test-data/ex1.bam has changed
diff -r 000000000000 -r 65edd5a6002e test-data/ex1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ex1.fa Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,56 @@
+>seq1
+CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCT
+GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCAC
+GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAG
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTC
+AGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAA
+CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACC
+AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT
+CTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
+ATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGC
+AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAAC
+AACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACAC
+ATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATAC
+CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCT
+TTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT
+TCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
+GCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT
+ACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGA
+ACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTG
+TGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTA
+CGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAG
+TCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC
+TTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTG
+TTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGG
+AGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATA
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTC
+TCCCTCGTCTTCTTA
+>seq2
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAG
+CTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT
+TATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTT
+CAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
+AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
+AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
+ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAG
+GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCAT
+CAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATT
+TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTA
+AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA
+ATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
+TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATA
+AAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACC
+TCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATA
+GATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATT
+AATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA
+AATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGT
+AAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATAT
+AACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAAT
+ACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGAT
+GATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG
+CGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATA
+GCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAA
+AAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAA
+TTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGC
+CAGAAAAAAATATTTACAGTAACT
diff -r 000000000000 -r 65edd5a6002e test-data/example.bam
Binary file test-data/example.bam has changed
diff -r 000000000000 -r 65edd5a6002e test-data/test.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.sam Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,7 @@
+@HD VN:1.6 SO:coordinate
+@SQ SN:chr1 LN:10
+read1 0 chr1 1 255 10M * 0 0 AACGTACGTA IIIIIIIIII
+read2 0 chr1 1 255 10M * 0 0 CACGTACGTA IIIIIIIIII
+read3 0 chr1 1 255 10M * 0 0 CACGTACGTA IIIIIIIIII
+read4 0 chr1 1 255 10M * 0 0 AACGTACGTA IIIIIIIIII
+read5 0 chr1 1 255 10M * 0 0 AACGTACGTA IIIIIIIIII
\ No newline at end of file
diff -r 000000000000 -r 65edd5a6002e test-data/toy.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toy.sam Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,14 @@
+@SQ SN:ref LN:45
+@SQ SN:ref2 LN:40
+r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
+r002 0 ref 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA *
+r003 0 ref 9 30 5H6M * 0 0 AGCTAA *
+r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC *
+r003 16 ref 29 30 6H5M * 0 0 TAGGC *
+r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
+x1 0 ref2 1 20 20M * 0 0 aggttttataaaacaaataa ????????????????????
+x2 0 ref2 2 30 21M * 0 0 ggttttataaaacaaataatt ?????????????????????
+x3 0 ref2 6 30 9M4I13M * 0 0 ttataaaacAAATaattaagtctaca ??????????????????????????
+x4 0 ref2 10 30 25M * 0 0 CaaaTaattaagtctacagagcaac ?????????????????????????
+x5 0 ref2 12 30 24M * 0 0 aaTaattaagtctacagagcaact ????????????????????????
+x6 0 ref2 14 30 23M * 0 0 Taattaagtctacagagcaacta ???????????????????????
diff -r 000000000000 -r 65edd5a6002e tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files. You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored. The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file. For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 65edd5a6002e tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Nov 17 07:30:30 2025 +0000
@@ -0,0 +1,7 @@
+
+
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+ value, dbkey, name, path
+
+
+