| Previous changeset 24:61ee47027bd3 (2018-11-15) Next changeset 26:0c16cad5e03b (2019-08-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652 |
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modified:
hisat2.xml |
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added:
test-data/hisat_input_1_split_forward.fastq test-data/hisat_output_spliced_1.bam test-data/novel_splicesite_out.tab |
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| diff -r 61ee47027bd3 -r 3fb01a8c902d hisat2.xml --- a/hisat2.xml Thu Nov 15 10:31:25 2018 -0500 +++ b/hisat2.xml Sat Jan 26 04:45:24 2019 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy3" profile="17.01"> +<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy4" profile="17.01"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> @@ -280,7 +280,11 @@ --min-intronlen ${adv.spliced_options.min_intron} --max-intronlen ${adv.spliced_options.max_intron} ${adv.spliced_options.tma} - + + #if str($adv.spliced_options.novel_splicesite_outfile) == "true": + --novel-splicesite-outfile '$novel_splicesite_output' + #end if + #if str($adv.spliced_options.notmplen): ${adv.spliced_options.notmplen} #end if @@ -523,6 +527,7 @@ <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks</option> </param> <param name="notmplen" argument="--no-templatelen-adjustment" type="boolean" truevalue="--no-templatelen-adjustment" falsevalue="" label="Disable automatic template length adjustment for RNA-seq reads" help="Default: false" /> + <param name="novel_splicesite_outfile" type="boolean" checked="false" label="reports a list of novel splice sites" help="Default: false" /> </when> </conditional> @@ -603,6 +608,13 @@ <expand macro="dbKeyActions" /> </data> + <!-- Novel Splice file --> + <data name="novel_splicesite_output" format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites" > + <filter>adv['spliced_options']['spliced_options_selector'] == 'advanced' and adv['spliced_options']['novel_splicesite_outfile'] is True</filter> + <expand macro="dbKeyActions" /> + </data> + + </outputs> <!-- Define tests --> @@ -616,6 +628,7 @@ <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> <param name="adv|reporting_options|reporting_options_selector" value="advanced"/> + <param name="novel_splicesite_outfile" value="false" /> <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> </test> <!-- Ensure advanced scoring options work --> @@ -770,6 +783,18 @@ <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" /> <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" /> </test> + <!-- Ensure novel splicesite file output works --> + <test> + <param name="type" value="single" /> + <param name="source" value="history" /> + <param name="history_item" ftype="fasta" value="phiX.fa" /> + <param name="input_1" ftype="fastqsanger" value="hisat_input_1_split_forward.fastq" /> + <param name="rna_strandness" value="R" /> + <param name="adv|spliced_options|spliced_options_selector" value="advanced"/> + <param name="adv|spliced_options|novel_splicesite_outfile" value="true" /> + <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" /> + <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" /> + </test> </tests> <help><![CDATA[ @@ -1072,6 +1097,10 @@ --no-templatelen-adjustment Disables template length adjustment for RNA-seq reads. + + --novel-splicesite-outfile + In this mode, HISAT2 reports a list of splice sites in the file : + chromosome name <tab> genomic position of the flanking base on the left side of an intron <tab> genomic position of the flanking base on the right <tab> strand (+, -, and .) '.' indicates an unknown strand for non-canonical splice sites. ----- |
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| diff -r 61ee47027bd3 -r 3fb01a8c902d test-data/hisat_input_1_split_forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat_input_1_split_forward.fastq Sat Jan 26 04:45:24 2019 -0500 |
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| @@ -0,0 +1,40 @@ +@phiX174_1980_2501_0:1:0_3:0:0_0/1 +TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1542_1965_0:0:0_0:0:0_1/1 +CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2950_3377_0:0:0_2:0:0_2/1 +CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2259_2739_1:0:0_1:0:0_3/1 +CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1141_1609_1:0:0_1:0:0_4/1 +TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_185_708_0:0:0_1:0:0_5/1 +CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1363_1914_3:0:0_0:0:0_6/1 +GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_3199_3732_0:0:0_1:0:0_7/1 +CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_36_572_1:0:0_0:0:0_8/1 +ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2128_2577_0:0:0_4:0:0_9/1 +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG ++ +2222222222222222222222222222222222222222222222222222222222222222222222 |
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| diff -r 61ee47027bd3 -r 3fb01a8c902d test-data/hisat_output_spliced_1.bam |
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| Binary file test-data/hisat_output_spliced_1.bam has changed |
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| diff -r 61ee47027bd3 -r 3fb01a8c902d test-data/novel_splicesite_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/novel_splicesite_out.tab Sat Jan 26 04:45:24 2019 -0500 |
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| @@ -0,0 +1,1 @@ +phiX174 2064 2162 . |