| Previous changeset 21:0b1c04a90182 (2018-07-14) Next changeset 23:6daca6da3059 (2018-09-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba |
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modified:
hisat2.xml |
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added:
test-data/hisat_input_1_interleaved.fasta test-data/hisat_input_1_interleaved.fastq test-data/hisat_input_1_interleaved.fastq.bz2 test-data/hisat_input_1_interleaved.fastq.gz test-data/hisat_output_1_noqual.bam |
| b |
| diff -r 0b1c04a90182 -r a26ed87f444c hisat2.xml --- a/hisat2.xml Sat Jul 14 09:06:59 2018 -0400 +++ b/hisat2.xml Tue Jul 24 09:29:27 2018 -0400 |
| [ |
| b'@@ -1,11 +1,12 @@\n-<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy1" profile="17.01">\n+<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy2" profile="17.01">\n <description>A fast and sensitive alignment program</description>\n <macros>\n <import>hisat2_macros.xml</import>\n </macros>\n <requirements>\n <requirement type="package" version="2.1.0">hisat2</requirement>\n- <requirement type="package" version="1.8">samtools</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n+ <requirement type="package" version="1.3">seqtk</requirement>\n </requirements>\n <stdio>\n <regex level="fatal" match="hisat2-align exited with value 1" source="both" />\n@@ -42,10 +43,10 @@\n #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n #set read1 = "input_f.fastq.gz"\n #set compressed = "GZ"\n- #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n #set read1 = "input_f.fastq.bz2"\n #set compressed = "BZ2"\n- #else if $library.input_1.is_of_type(\'fasta\'):\n+ #elif $library.input_1.is_of_type(\'fasta\'):\n #set reads_are_fastq = False\n #set read1 = "input_f.fasta"\n #else:\n@@ -56,24 +57,24 @@\n #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n #set read2 = "input_r.fastq.gz"\n #set compressed = "GZ"\n- #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #elif $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n #set read2 = "input_r.fastq.bz2"\n #set compressed = "BZ2"\n- #else if $library.input_2.is_of_type(\'fasta\'):\n+ #elif $library.input_2.is_of_type(\'fasta\'):\n #set read2 = "input_r.fasta"\n #else:\n #set read2 = "input_r.fastq"\n #end if\n ln -f -s \'${library.input_2}\' ${read2} &&\n \n-#else if str($library.type) == \'paired_collection\':\n+#elif str($library.type) == \'paired_collection\':\n #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n #set read1 = "input_f.fastq.gz"\n #set compressed = "GZ"\n- #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #elif $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n #set read1 = "input_f.fastq.bz2"\n #set compressed = "BZ2"\n- #else if $library.input_1.forward.is_of_type(\'fasta\'):\n+ #elif $library.input_1.forward.is_of_type(\'fasta\'):\n #set reads_are_fastq = False\n #set read1 = "input_f.fasta"\n #else:\n@@ -84,24 +85,44 @@\n #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):\n #set read2 = "input_r.fastq.gz"\n #set compressed = "GZ"\n- #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #elif $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n #set read2 = "input_r.fastq.bz2"\n #set compressed = "BZ2"\n- #else if $library.input_1.reverse.is_of_type("fasta"):\n+ #elif $library.input_1.reverse.is_of_type("fasta"):\n #set read2 = "input_r.fasta"\n #else:\n #set read2 = "input_r.fastq"\n #end if\n ln -s \'${library.input_1.reverse}\' ${read2} &&\n-\n+#elif str( $library.type ) == "paired_interleaved":\n+ #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set interleaved_reads = "input_f.fastq.gz"\n+ #set compressed = "GZ"\n+ #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set interleaved_reads = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #elif $library.input_1.is_of_type(\'fasta\'):\n+ #set reads_are_fastq = False\n+ #set interleaved_reads = "input_f.fasta"\n+ #else:\n+ #set interleaved_reads = "input_f.fastq"\n+ #end if\n+ ln -f -s \'${library.input_1}\' ${interleaved_reads} &&\n+ #if $library.input_1.is_of_type("'..b' </param>\n \n <when value="single">\n@@ -368,6 +394,10 @@\n <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="Must be of datatype "fastqsanger" or "fasta"" />\n <expand macro="paired_end_options" />\n </when>\n+ <when value="paired_interleaved">\n+ <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTA/Q file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/>\n+ <expand macro="paired_end_options" />\n+ </when>\n </conditional>\n \n <!-- Summary Options -->\n@@ -709,6 +739,38 @@\n <param name="summary_file" value="true" />\n <output name="summary_file" file="hisat_output.summary" ftype="txt" />\n </test>\n+ <!-- Ensure interleaved input works -->\n+ <test expect_num_outputs="1" >\n+ <param name="type" value="paired_interleaved" />\n+ <param name="source" value="history" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n+ <param name="input_1" ftype="fastqsanger" value="hisat_input_1_interleaved.fastq" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ </test>\n+ <!-- Ensure interleaved bz input works -->\n+ <test expect_num_outputs="1" >\n+ <param name="type" value="paired_interleaved" />\n+ <param name="source" value="history" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n+ <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ </test>\n+ <!-- Ensure interleaved gz input works -->\n+ <test expect_num_outputs="1" >\n+ <param name="type" value="paired_interleaved" />\n+ <param name="source" value="history" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n+ <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_1_interleaved.fastq.gz" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ </test>\n+ <!-- Ensure interleaved fasta input works -->\n+ <test expect_num_outputs="1" >\n+ <param name="type" value="paired_interleaved" />\n+ <param name="source" value="history" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n+ <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />\n+ <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" />\n+ </test>\n </tests>\n \n <help><![CDATA[\n@@ -1077,7 +1139,6 @@\n \n --non-deterministic\n Normally, HISAT2 re-initializes its pseudo-random generator for each read. It seeds the generator with a number derived from (a) the read name, (b) the nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed` option. This means that if two reads are identical (same name, same nucleotides, same qualities) HISAT2 will find and report the same alignment(s) for both, even if there was ambiguity. When `--non-deterministic` is specified, HISAT2 re-initializes its pseudo-random generator for each read using the current time. This means that HISAT2 will not necessarily report the same alignment for two identical reads. This is counter-intuitive for some users, but might be more appropriate in situations where the input consists of many identical reads.\n-\n ]]></help>\n <citations>\n <citation type="doi">10.1038/nmeth.3317</citation>\n' |
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| diff -r 0b1c04a90182 -r a26ed87f444c test-data/hisat_input_1_interleaved.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat_input_1_interleaved.fasta Tue Jul 24 09:29:27 2018 -0400 |
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| @@ -0,0 +1,40 @@ +>phiX174_1980_2501_0:1:0_3:0:0_0/1 +TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA +>phiX174_1980_2501_0:1:0_3:0:0_0/2 +GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA +>phiX174_1542_1965_0:0:0_0:0:0_1/1 +CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA +>phiX174_1542_1965_0:0:0_0:0:0_1/2 +CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCT +>phiX174_2950_3377_0:0:0_2:0:0_2/1 +CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA +>phiX174_2950_3377_0:0:0_2:0:0_2/2 +GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC +>phiX174_2259_2739_1:0:0_1:0:0_3/1 +CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT +>phiX174_2259_2739_1:0:0_1:0:0_3/2 +GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGACGAAGACTCAAAGCGA +>phiX174_1141_1609_1:0:0_1:0:0_4/1 +TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT +>phiX174_1141_1609_1:0:0_1:0:0_4/2 +CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCTAGAA +>phiX174_185_708_0:0:0_1:0:0_5/1 +CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT +>phiX174_185_708_0:0:0_1:0:0_5/2 +TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATGTTGACGGGATGAACATAATA +>phiX174_1363_1914_3:0:0_0:0:0_6/1 +GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC +>phiX174_1363_1914_3:0:0_0:0:0_6/2 +TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT +>phiX174_3199_3732_0:0:0_1:0:0_7/1 +CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA +>phiX174_3199_3732_0:0:0_1:0:0_7/2 +TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCATTGATTTGGTCATT +>phiX174_36_572_1:0:0_0:0:0_8/1 +ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC +>phiX174_36_572_1:0:0_0:0:0_8/2 +TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT +>phiX174_2128_2577_0:0:0_4:0:0_9/1 +TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG +>phiX174_2128_2577_0:0:0_4:0:0_9/2 +CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTATCAAAATATAACGTTGACGAT |
| b |
| diff -r 0b1c04a90182 -r a26ed87f444c test-data/hisat_input_1_interleaved.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat_input_1_interleaved.fastq Tue Jul 24 09:29:27 2018 -0400 |
| b |
| @@ -0,0 +1,80 @@ +@phiX174_1980_2501_0:1:0_3:0:0_0/1 +TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1980_2501_0:1:0_3:0:0_0/2 +GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1542_1965_0:0:0_0:0:0_1/1 +CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1542_1965_0:0:0_0:0:0_1/2 +CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2950_3377_0:0:0_2:0:0_2/1 +CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2950_3377_0:0:0_2:0:0_2/2 +GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2259_2739_1:0:0_1:0:0_3/1 +CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2259_2739_1:0:0_1:0:0_3/2 +GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGACGAAGACTCAAAGCGA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1141_1609_1:0:0_1:0:0_4/1 +TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1141_1609_1:0:0_1:0:0_4/2 +CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCTAGAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_185_708_0:0:0_1:0:0_5/1 +CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_185_708_0:0:0_1:0:0_5/2 +TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATGTTGACGGGATGAACATAATA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1363_1914_3:0:0_0:0:0_6/1 +GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1363_1914_3:0:0_0:0:0_6/2 +TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_3199_3732_0:0:0_1:0:0_7/1 +CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_3199_3732_0:0:0_1:0:0_7/2 +TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCATTGATTTGGTCATT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_36_572_1:0:0_0:0:0_8/1 +ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_36_572_1:0:0_0:0:0_8/2 +TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2128_2577_0:0:0_4:0:0_9/1 +TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2128_2577_0:0:0_4:0:0_9/2 +CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTATCAAAATATAACGTTGACGAT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 |
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| diff -r 0b1c04a90182 -r a26ed87f444c test-data/hisat_input_1_interleaved.fastq.bz2 |
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| Binary file test-data/hisat_input_1_interleaved.fastq.bz2 has changed |
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| diff -r 0b1c04a90182 -r a26ed87f444c test-data/hisat_input_1_interleaved.fastq.gz |
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| Binary file test-data/hisat_input_1_interleaved.fastq.gz has changed |
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| diff -r 0b1c04a90182 -r a26ed87f444c test-data/hisat_output_1_noqual.bam |
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| Binary file test-data/hisat_output_1_noqual.bam has changed |