# HG changeset patch
# User iuc
# Date 1655286305 0
# Node ID 44f6ec903688f788a8f6a0086ffa7417466c049d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
diff -r 000000000000 -r 44f6ec903688 clair3.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/clair3.xml Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,311 @@
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+ 0.1.11
+ 0
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+ clair3
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+ output_options['selection_mode'] == 'advanced' and output_options['pileup_check']
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+ output_options['selection_mode'] == 'advanced' and output_options['full_alignment_check']
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+ output_options['selection_mode'] == 'advanced' and output_options['phased_bam_check']
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+ 10.1101/2021.12.29.474431
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diff -r 000000000000 -r 44f6ec903688 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,10 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+test1 "Test Genome" ${__HERE__}/test1.fasta
diff -r 000000000000 -r 44f6ec903688 test-data/clair3_models.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clair3_models.loc Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,10 @@
+#Enter the model names in the second column, the platform name in the second and the path in the third.
+#This file lists the locations and dbkeys of all the model files
+#under the "models" directory (a directory that contains a directory
+#for each build). This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_model.loc could look something like this:
+test_model "the_model_name" ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422
diff -r 000000000000 -r 44f6ec903688 test-data/full_alignment_1.vcf
Binary file test-data/full_alignment_1.vcf has changed
diff -r 000000000000 -r 44f6ec903688 test-data/merge_output_1.vcf
Binary file test-data/merge_output_1.vcf has changed
diff -r 000000000000 -r 44f6ec903688 test-data/phased_bam_1.bam
diff -r 000000000000 -r 44f6ec903688 test-data/pileup_1.vcf
Binary file test-data/pileup_1.vcf has changed
diff -r 000000000000 -r 44f6ec903688 test-data/test1.bam
Binary file test-data/test1.bam has changed
diff -r 000000000000 -r 44f6ec903688 test-data/test1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.bed Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,3 @@
+chr1 14756 15038 JUNC00000001 294 - 14756 15038 255,0,0 2 73,69 0,213
+chr1 14969 15836 JUNC00000002 144 - 14969 15836 255,0,0 2 69,41 0,826
+chr1 15905 16677 JUNC00000003 12 - 15905 16677 255,0,0 2 42,71 0,701
diff -r 000000000000 -r 44f6ec903688 test-data/test1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.fasta Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,85 @@
+>demo20
+TGCCTGCTTTGTGCCAGGTTCTGGGTTGGGAGGTGCTGGGGACAGGGAGATGAGTCAGAC
+CTgggaagatttcgtagaggaggtgacagtaagctggaacctgtgtaatgagcaggagtt
+gcccagtggagaaggggaaggtgttccaggcggaagaaacagcatatgcaaaggccccaa
+ggtaggaagggccctagtgtgtgcagaggacagggcatggggaggggaactaaggctgag
+gccaaggagaggaaatgactcacaccgtgagagaggagttgagaccagggaggCTGCTTG
+CTGTATGATGCAACTGAGAGGGTAGAACAAGGCTGGCACAGAGAAGGTGGGGAAGGAAAA
+GGAGAGACGAAGCTGAGATTTCAGCAGGGCCAAGTCAGCCGTGAGTGCCAGGCTGCGGAG
+CCCAGATTCTCTGGGCTGagaaagagcactctgtccagagtgtggaggggggcctggagg
+ggatgagactcaaagctgggaggccagagaggaggctgctagagttttctgggagagagt
+tactggggcctgaacTCCAGTGAGGCActtcccatttcacagaccaggaaactgaggccc
+aagagtgaggcaactggcccaagggcacacagccaggtaaggcagaacCTTCCTTCTTTG
+GAGCTCCCTTGGGTGGGAAGCTGTGGGCTCCCCTTCATAGCCCACCCTTTTGGCTGTATC
+TCCCTGCTGCCCTGGGCATATGCTCCCTTATTCTGTCCTCCCTTGAAGCTGACTGCTGGC
+CTTAAAGGGCCCCTGTTTCTTCCCTCTGGACTACATGAGATCGGGATAGTATTAATGACT
+AAAACCTACCAGGGGTTTCTAGGCCTGGCCTGGAAAAAGTGACTGTTGACAAACAAAGTG
+CAGAGATTTAAAATCTCCTCTGTCTCAATTAGTGGAATCCAGTTAGAGGTTTGAACTATG
+ATTCTACCAGAATCCAATCTCTCTGGGTAGCCAGGTACCCAGGATGGGGCTAAAATTCCA
+GATGGATAGGTTGTCAACACCAGTGAGGAACCAGGAGGCTACCACAGGGTGGGACTTCCT
+GGTTTGGCTTTACATCTGAACTTCAGGGATCCCAGATCCTGGATCTGGGGCACTTGTCCA
+GAGAAGGCTATTGCTCTCATGTCACAAATGAGATGACTAAGACCCCCAAATCAATTCCAG
+TTCACTCACAAGCATTTCCTGGGCAGTGGAGACCCCTGCCCCACCTGTTGGCACCCCCTC
+AGCTCCCCACAGGGAATTGGAGTCCAGCCAAGCATGAGGAGGCTGTTGGCCTCAAGGTGA
+GCAGGGATGGGCTGAACCTCACCCAGTAAGGCAAGGACAGAGCCAGGGTTGGCCTGAGAT
+TTCCAGCCACCCTTTCCAAGGCTCTGCTCACTGTTATTTTCCTTAGTCTacaacaatatc
+aataacaataacaacaataatatcaacaCAAAAAGTGAAATACTCACCATGTATTGTAGT
+GTTTCCAAGGTGTCATGTAATGCCAGGGGTAGTTTGGGGCCAGGAAAAATATTTTTGGGA
+GGCATAAGAATAGGATGGACTGATATTGATATGCAACAGTTTGATCTGGTCCTCCTCTGA
+ATATCTGGGCTGGTAATTTGTACCAGTTTCCCTCGCTTTtgtgcataggcactgtgctga
+acccttttgtatgcatgaactcatccgattctctgtgcaagaactctatgagattattat
+tcccgttttacaagtaagaaaaattgaggctctgagaagttaaataaatgacttgtatga
+agttccagtgctaattaataagtgaaggagccagggcttgaactccggcccatctgactg
+caaagccagtgcccttcctcctacacATCTTCCTTTGGATTTCCACCACTGAGCATATGT
+AAGGTTGGGCAAACAGCCTGCATGAACAATCGCTGCTTTTATATCATGCACAAGTTTGGT
+CTTTTCTGCCTGTGCCCATGTCCTTGTAACCTTCTGAACCAAACTCCCCAGTGCCTGGGA
+ACATCAGAAGACTTGACTCTCTTCTCCTTTCACTAGCCTCCACCTGACTGGGACAAAGCC
+ATGCAGAGAGCTAGTGCTCCCTTCCTGCTAGACTTCAAGGATGCCTGGTTCCTGTGCCCC
+ATCTCCATCCAGCCCTCTCTTCTACACCTGGTGACTGAGCCTCTCCTTCAGTTTCTCCAT
+CCAGAAGGGGGTGAAAGCAACTGCCTAGTGTCCTTCCCTGGTGATAGTGGAGCACGGGGG
+ACAGGGTGTTTGGGCAAAAGGTGCCCAAGGTGAGGTGCCCAACACAACCTCCTACTCAGA
+CGATTGAGCAGACATTCAGCCTCATCTGGGGACTGGGTTACCAGTGGGTTAGTGGGAGGC
+ATTGGGCCCAGGCCCTGTGCCTTGGGCTGAGCTACAAGAAACCCACACATGGGATGAATT
+CAGGCAGCTCAAGGCCAGGTCTGTGCATACGCCAGTAATAGGTTCAGGTTAATCCACATG
+TCGCGATTTGGAAGGTGTCTACTTTTCCTACCTGTAGCTTCCTTAGGCCTCAAACCCCTA
+CTCAGCTGGGTCTGCCAGACTGAGATGGAGCCAGGGTGGAATCTTCTGCCCTCAAATCCC
+TGTCAGCCCTGGTGGTGCCGGGAGCGCCATCACTATTGGGTCTTAAAGGCTTTCCAGCCT
+TCCACTATGGATCCAGGAGCAGCAGTAGCCCCTTTGGTCTTTCTCTCTCATCAGGACATC
+TCCACTCATGGTTCCAGTCAGAGCTTCTTGAAAGTAGTCCCACTCTGTTCAAAAGCCTCC
+CATGCCCCCTGCTAGCCTCAGGCTAAGAGCCCTTCTCCTTCGCACAGCCTTTGGACCTGT
+CTATTTTTATGGTCTGGAAACTTCAGGAACACTGATAGCTGAGCATCTGGCACATATTAT
+GCACTCAAAAACCATGTATTTCTTTCTCCTTCCCTTTGGGACCCGTAAACCAGGGactgg
+acatttttgcaagagacaggagctgtgactgtgcattcactgctgtatccccagcaccca
+gcactgggcctgccacacagtaagtgcttagtaaatgtttgttgactgagtgaTTGCAGC
+TGGGGCCAAGAATGCCTTGGACACCCCAAGTAGGCCGTGTTAGAAGGAGTCAGTGAGAGC
+CTGGGAGCCCAGCCCAGAATTGTTTTCTTGACCCAGAAGCCAGGGCCAGGGATGCCTCTT
+CACTTCTGTTTGGCCCTCTTGGGCTTAGGGGCAGGGGCATTAAGATGAgagaggtccttg
+gggtgcattgagtctaacctcccagttcctcccattctacagccaggaaaactgaggccc
+agggaggggtaggacaagcccaagAAAGTGGGGCTGGAGAATGAATCCTGGAGACCAAAC
+TTGTCAGTCTGGATTGCTGTTGCCCTCATCCTCGCCTCCAAAACCCatgggtaaactgag
+gccaagagaggggcaggggcatgcccaaggtcacccatggaatcaggggacagggcctgg
+attgggattgttgttgacgccattattactgtttattgttgtttctatttcacAGATGGT
+CGGGGAGGGTGGGGCCCGCAATGGCTCCCAGGCGCCCAGAGACCCTGGAGGGTGAGCAGG
+GTCTCCCCTCCCCTCTCCTGCCCGTCTTTAGCCACACTGGGGCGCACACCGCTCACTCAC
+CCGGGGCCGAGGCGTTAGCCCTTTCTTGCACCAGGTGCCGCAACAACACCAGCAGCTGGC
+GCAGGCTGTGCTGCTGGTCCTGCAGGAGGCTGGAGTTGTGCCTGACACCGCGCAGGCCGC
+GCTCGATGTTGGTGAGGGCGGCGCTCTGGCGGCTCAGCGTGTTCAGCAGCTTCGCCTTCT
+TGCTGAGGATGCTGGCCAGCTCCTCCTGCTGCTTGGTCTCCAGGGCCTGCAACCGCTTCT
+CGAGCGCGCTGCGGGGTAGGGGGCGCACAGAGGTGAGCCTGGCATCCTCGCGAAGCACGC
+ACCCCCGCGCGCCTCCCCGGCCCTGGAGTCCCTGCAGCCCGACGATGAGACTCAAGTGTG
+GTGGAACGTCCTGTGCCCACTGTAGGCACAGATTGAGGAGGGGAGAAAAGAGATACCCGG
+CCCTGGAGTAATATAGATTGAGGTTTAGTGGAAGAAAGAGGTGGTGTGGGAGGGACACCA
+GCAACTGGGTAGCTATTATCAAATCCCAACTGTGCTTGCTTTTTGACCCAGCAGTCTACT
+CTCAGGAGTTATCCTCTAGGGAGCATGGTCAAGAATGGCCCTGGGGACTTGCTTGTAATA
+GAAAAACAAACTAACCAACCAACCAAAAAAGATATAGCCTAGATGCCCAAAAGCCAGGAC
+TGGCTGAATCCGTTGCGTTTTGGCGTCCCTGGAAATGTTCCGCAGTCATGAAGGAGGAGG
+CATTTGCACAGAATTGGAAAGATGCCCAGGACTTGGGGCACATCAAGCCTAACCCCATGT
+GTGGCAAGAGAAGAAAGAAAGTATTAATGTAAATAAAGAGAAATGGGGTGAACATATAGG
+AGAAGGCTGGAAAGACCGCAGTGGTGCCTGTGTTTGGGAAGAATATGAAAGAAATTCCCT
+CAAGTGCTGTGACTTCTGCAGAGCAGGTTTGAGTGGATGAAGATGGAGAGGAGGAAGATG
+GGGGCAGGATGGAGGGCCCAACTTTCACTTTTATTTTGTACAGGTTCCTGTTGTCCGATG
+ATATTATAATAATCAAGAGACATTTTTTGTAATGGATTTAGAAGCAAAGAGGAGTTTTTC
+AAAAGAAAGCCTTAGACTCAGCTCTTTCTTTTTGGACATTTTATCCTCCAGATTTACTca
+catgtgtgtgaaatgagatatggaaatgttactcatcgtatcactggttggattagtaaa
+aggctggaagcaacctcaatatccattaactggggactggaggaataaaagcagggacca
+catatggtggagcattataa
diff -r 000000000000 -r 44f6ec903688 test-data/test1.vcf.gz
Binary file test-data/test1.vcf.gz has changed
diff -r 000000000000 -r 44f6ec903688 tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,10 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#test1 Test-Genome ./test-data/test1.fa
diff -r 000000000000 -r 44f6ec903688 tool-data/model.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/model.loc.sample Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,10 @@
+#Enter the model names in the second column, the platform name in the second and the path in the third.
+#This file lists the locations and dbkeys of all the model files
+#under the "models" directory (a directory that contains a directory
+#for each build). This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_model.loc could look something like this:
+#test_model "the_model_name" r941_prom_hac_g360+g422 $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422
diff -r 000000000000 -r 44f6ec903688 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,12 @@
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+ value, name, platform, path
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diff -r 000000000000 -r 44f6ec903688 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Wed Jun 15 09:45:05 2022 +0000
@@ -0,0 +1,13 @@
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+ value, name, platform, path
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