| Previous changeset 0:30fc9f2bcbe4 (2021-01-19) Next changeset 2:b4b6b660293a (2022-07-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c" |
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modified:
irissv.xml macros.xml test-data/all_fasta.loc |
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added:
test-data/genome.fa.gz |
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removed:
test-data/genome.fa |
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| diff -r 30fc9f2bcbe4 -r 1d4f065fa0ef irissv.xml --- a/irissv.xml Tue Jan 19 20:30:21 2021 +0000 +++ b/irissv.xml Mon May 17 17:29:39 2021 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>Refine insertion sequences</description> <macros> <import>macros.xml</import> @@ -12,7 +12,7 @@ @REF_FASTA@ iris - genome_in=reference.fa + genome_in=reference vcf_in='${in_vcf}' reads_in='${in_bam}' vcf_out='${out_vcf}' @@ -74,7 +74,7 @@ <test expect_num_outputs="1"> <conditional name="reference_source"> <param name="reference_source_selector" value="history"/> - <param name="ref_file" ftype="fasta" value="genome.fa"/> + <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/> </conditional> <param name="in_vcf" value="sniffles.vcf"/> <param name="in_bam" value="iris.bam"/> |
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| diff -r 30fc9f2bcbe4 -r 1d4f065fa0ef macros.xml --- a/macros.xml Tue Jan 19 20:30:21 2021 +0000 +++ b/macros.xml Mon May 17 17:29:39 2021 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.0.4</token> - <token name="@PROFILE@">18.01</token> + <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="1.9">samtools</requirement> @@ -29,9 +29,16 @@ <token name="@REF_FASTA@"><![CDATA[ #if $reference_source.reference_source_selector == 'history': - ln -f -s '$reference_source.ref_file' reference.fa && + #set reference = $reference_source.ref_file + #set ext = $reference.ext #else: - ln -f -s '$reference_source.ref_file.fields.path' reference.fa && + #set reference = $reference_source.ref_file.fields.path + #set ext = $reference_source.ref_file.fields.path + #end if + #if $ext.endswith('.gz'): + gunzip -c '$reference' > reference && + #else: + ln -sf '$reference' reference && #end if ]]></token> @@ -51,7 +58,7 @@ </param> </when> <when value="history"> - <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> + <param name="ref_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> </when> </conditional> </xml> |
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| diff -r 30fc9f2bcbe4 -r 1d4f065fa0ef test-data/all_fasta.loc --- a/test-data/all_fasta.loc Tue Jan 19 20:30:21 2021 +0000 +++ b/test-data/all_fasta.loc Mon May 17 17:29:39 2021 +0000 |
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| @@ -16,4 +16,4 @@ #fasta file. So there will be multiple fasta files for each build, #such as with hg19 above. # -iris iris iris ${__HERE__}/genome.fa \ No newline at end of file +iris iris iris ${__HERE__}/genome.fa.gz |
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| diff -r 30fc9f2bcbe4 -r 1d4f065fa0ef test-data/genome.fa --- a/test-data/genome.fa Tue Jan 19 20:30:21 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1583 +0,0 @@\n->chr1\n-AATATGCCCATATTACAGATAAGAAAATTAAAAATTAAGGCTTACAGAGTTTATTACATGCTTATAGATG\n-GACCTAGGGTAATGTTGGATACTTAGAGTGGGATCACATTAAAGCCTCTACAGCAGTGGTCCCCAACCTT\n-TTTGGCACCAGGGACCGGTTTTGTGGAAGATAATTTTTCCACAGACGGGGGTGGAAGTGTATGGTTTCGG\n-GATGAAACCGTTCCATCTCAGATCATCAGACATTAGTTAGATTCTCATAAGGAGCGGGCAACCTAGATCC\n-CTCACATGTGCAGTTCACAATAGGATTCATGCTGGTATGAGAATCTGATGCCGCCACTGATCTGACAGAT\n-GCTCGCCTGTTGCTCACCTCCTCCTGTGTGGCCTGGTTCCTAATAGGCCATGGACAGTACCGGTCTCTGG\n-CCCAGGGGTGGGGCCCCCTGCTCTACAGCATTCTACTTCATCGGTAAAATCTTTGAAAATGTCTTCTAGA\n-AATATTTTTAAGGTCACTTTACCTTTTGATCATTGAATATTGGGTCAATTTTGTTGTTGTTGTTGTTGTT\n-GTTGAGACAGGGTCTCGTTATGTTGCCCAGGCTGGATGGAGTGTGGTGGTGCAGTAACGGCTCACTGTAG\n-CTTCAACTTCCTGGGTGCAAATGATCTTTCTGCCTCAGCTTCCTGAATAACTGGGACTACAGGCGCACGC\n-TACCATACTTGGCTAATTTTTTGTATTTTTAGTAGAGATAAGACCTCATTATGTTGCCCAGGCTGGTCTC\n-AAACTCCTGGGCTCAAGTGATCCTCCTACCTCAGCCTCCCAAAGTGCTGAGATTACAAGTGTGAGCTACT\n-GTGCTCAGCTGACATAATCTTTTGATGTATGAATGGACCCATCTCTCTTGCTGCCCCTGCAACACCAGAT\n-ACTGGGACTCATCGATTTCTGATGATGAAAGATGTCGTTCTCATGGGAGTCTTTATGTTATACAAATGGA\n-GAGCAAAGTTCCCAAACATGCTGCCGTGGTTGATGTGTTCTGTCATCTGGTAATAACTGGAGTTATTACA\n-GTCATCCAAGTGAGAGAAGTGGTGGTTGAACCAGGGTGGTCACGATGGTGGTGGGGAGAAGCCATATTTG\n-GAAAGTAGAACTGATAGGATACATCAGATGTGGAGGATGAAAGAAAAAAGCCAAAGATGGCTCCCAGATC\n-ATCTGTGGAATGTTGCTTGTAGGGTCCAGGTCTGGAGTATGCTGTGTGTCCAGAGCAACCTAGATTGAAG\n-AAAAGACCTCAGGCACAGAAGCTGTAAAAGAGGCCTTGAAAAGCAGCTTGAAAAGGTGGATTATAGGAAG\n-TAAAACAATATGAAGTCTATAATACTTTTAAAAGAGTTATTTTCTGACACTAGTCCTCAAAAATATTCCT\n-GGAGTCCATTCTTTGCAGGAAAAGTGGCGACTTGTCCTAGACAAAGCCTACGTGCTGATTCCATGTGACC\n-CTGGGGGTGGGTACTAAATTCGTAACAGCTTGTGGGTGAAAATATGGTTTATATGTTGAATGTGTTCCTT\n-AATTACTGTAATTCTGTTTTTATGTGCATGGTTTCTGTGAAACAAATTAGAAGTCCAACACACTATTTTA\n-GCTCAGTTGACCTTGATACAAGAACTGCTGTGTTAATTATGCCCAGTCTTTCAGTAGTACAATCCTCTTT\n-TTTTTTTCTGTGAATGTTAGTAAAATCTACTGGTATTTTATGTATATATTGCACAGCTATACACTGTTTT\n-TCTTTTTATGCTCTTGAAAATGGAATTTAATCAGAGTTGTACATGACACATGGAGGGCATTCATTTGAGT\n-CCTTGGTATAGGGCAGTATAGAGGATCCATAAGACATGGTCCAAGCACTTTGAGGATATATGATGTTGGG\n-GGAGCATCAGAGATTTGTTGACACATTTAAGTAAGGACTTGAATGTCGTACTTTGACTGTTGGCAAGAAA\n-TAGGCTCTTGGCTGGGTCCAGTGGCCCACACTTGTAATCCTAGCACTTTGGGAGGCCAAAACAGGAGAAT\n-TGCTTCAGCCCAGGAGTTCGAGACCAGCTGGAGCAACCTAGGGAGACCCTGTCTCTACAAAAAAATAAAC\n-AAATTAGCCGTGCATGGTGGCACGTGCCTGTGGTCCCAGTCACTCAGGAGGCTGAGGTGGGAGGATCACT\n-TGAGCCCAGGAGGCTGAGGATGCGTGAGCTGTAATCTCACCACTGCACTCCAGCCTAGGGCGACAGAGCA\n-AGACCCTGTCTCTAAAAGAGAAAAGAAACAGAATTCTTACATTGTGCTTTAGTTTATCAGTTAGTGAACT\n-TTTCTTTTTTTGTTGTTGCTTTTTATTTTTTGTGGAGATGGGGTCTCACTATGTTGCCCAGGCTAGTCTC\n-GAACGCGTAGGCTCAGATGATCCTCCCACCTTGGCCTCCTAAAGTGTTGAGATTACAGGCATGAGCCACT\n-GAACCTGGGCCTGGTGTGTTTTTCTTACCTTGGTTTAAAGATCAAATGGAATATTATCATACCTACTGAA\n-TATTGAGAGTTTAAAACAGGGTAAAATACGTATTTAAGAAAAATTAACGTATGTGTAAGTGTTTCACTCC\n-TTTAATTCTGTAAACTAGGTATTACCTCAATTTTAGAGACGACACAGACGTGCAGTCATACCCAAGGTCG\n-TAAAAAACACCTAAATACAGTATTTCTTAACTTTTTTTTTTTTTTTGAAACGGAGCCTCGCTCTGTTGCC\n-CAGGGTGGGGTGCAGTGGTGCAATCTCAGGTCATTGCAACCTCTGCCTTCTGGTTTCAAGCAGATCTCTT\n-GCCTCAGCCTCCCAAGTAGCTGGGGTTACAGGTGCCCACCACCACGCCCAGCTAATTTTTGTAAATACAG\n-TATTTTTAAATTGTTCTTTCATATGTTTAGAATATTAAGCCAGGCATGGTAGCCCATGACTTTGGGAGGG\n-CAAGGAAAGAGGATTGCTTGAGCCAAGAGTCTCAGTCCAGCCTAGGCAACATGGCAAAGCCCCATCTCTG\n-CAAAAAAAATTAAAATTTGGCTTGGCATGGTAGTGCACACCTATAGGCCCAATTACTTGGGAGGCAGAGG\n-TGAGAGGTTCACTTGAGCCCAGGAGTTGCAGGCTGCAGTAAGCCATGATTGAGCCACTGTACTCCAGCCT\n-GGGTGACAGACCGTGACGCTGTCTGGGGAAAACAAATGGATTAGTTGTTGATAGAAGCAGTTATTCTAAA\n-AGCAGCTTGGGGGCGGGTGCAGTGGCTCACACGTGTAATCCTAGCAATTTGGGATGCCGAGGCGGGTGGA\n-TCACCTGAGGTAAGGATCCTGTTCAAGGCCAGCCTGGCCAACATGGTGAAACCCTGTCTCTAGTAAAATA\n-CAAAAATCAGCCAGGCATGATGGCGGGTGCCTGTAATCCTAGCTACTGGGGAGGCTGAGACAGGAGAATC\n-GCTTGAACCTAGGAGACAGCGGTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCAGCTGA\n-GCTAGACTGTCTCAAAAAAATAAATAAATAAAATAAAAGCAGCTTGGTTTTGAAGATATAAGTTAGGAAA\n-ATCTATTAGTTTCAGAAGCTTTAAAAGTCTGGGAGAAAGGAATATTGAAGAAGAGGAAAAGGATTTCATG\n-TGAATTGAGGAAGTTAACTCATTGGTGTAGTTTTTCCTTTCTTTTTTTTTTTTTTTACTAAGGAAAAGAG\n-AACAAAGCGATAAAATCTGAGTAGTCTTTCAGTCATTCTTGGTAGAATTGGTAGCTAAAAGGCTGAGTGA\n-AATATGGCTTAAAAGCTTTATTGGCTGGGCGCGGTGGCTCACCCCTGTAATCCCAGCACTTTGGGTGGCT\n-TAGGTGGGTGGA'..b'AAATTATGAGGAAAAAGCTGCGGGGAAGGGGCAGATGATTATCAGTTTACATGTCTTT\n-GGGCATTTTAGGTAGAGTGAAATCTAGGCCTTGCAAATCATATCTCTTTAGAATCATTCAAAATTTGCTT\n-AGGAAGAGCAGAATTGTTGATTGTTTATTCAATGTGTATGCTAAGTAACATGTTTTATAGAAGAGTTATA\n-ATTTTTTTCCTATTTTCCTATTGTATATTTGTTTTTTAATACTCTGGGATCAAGTATACAGTGAATATGT\n-ATAGTACATTTATCCCTGTTTTATAAAAAAATGGGAAACTAAATTTGTTGTAAATGATTAAGGAACTTTA\n-TGATTATAGATCTTTTGCTCAAATCTTTATGGCAATAGGTTTTACTATGTTTCTATATTGTGAGGAGGGG\n-AGCGAGTTGCCTGTGGGTTTTGGTTTTATGGTTTTAAAATATAAGCAGTGTATAAAATATTTTTATTGTG\n-TGCCATTTTTCTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCAGG\n-CTGGAGTGCAATGGCCCGATCTCGGCTCACCGCAACCTCCGCCTCCCAGGTTCAAGCAATTCTCCTGCCT\n-CAGCCTACCAAGTAGCTAGGCTTACAGGCATGCACTACTACGCCCGGCTAATTTTTGTATTTTTAGTAGA\n-GACAGGGTTTCCCCATCTTGAGGCTGGTCTCGAACTTCTGACCTCAGGTGATCCGCCCGCCTCAGCCTCC\n-CAAAGTGCTGGGATTACAGGCCTGAGCCACCGCGCCCGGCCCTCCTTTTTTTTTTTTTTTGAGACGGAGT\n-CTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCTGCTCACTGCAAGCTCCGCCTCCCGGGTT\n-CACGCCATTCTCCTGCCTCGGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACCACGCCTGGCTAAT\n-TTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTTTTAGCCAGGATGGTCTCAATCTCCTGACTTCGTG\n-ATCCGCCCGCCTCGGCCTCCCAAAGGACTGGGATTACAGGCATGAGCCACCGCGCCCGGCCGCCATTTTT\n-CTTAATTGTTGCTCTAGGAGGCTTTTAGAGCGGAAGATTGTGCTGAAGATGTCACTGGGATTTTTAACAA\n-GCCCTAAACGTGCTTGGTTACTAAAGTTAATATAAAGTTACAGTGTTGCCACACAGATAACATCAATTAT\n-AGTTGCAGGCAAAATCTTTAGTAGTTTGCCAACAACAGTATAATTACTAGACACTGAGATATTAGATAAA\n-TTTATTCTGGGGAATTAAAAGGCGTTTAAATACTAATCTTGTTTTGACTGCCTTATTTTCTAGGGCTCAG\n-TAATTAAAGTGTTATTTCTGCATCTTTATGCTAAAGTAGCAAAGTTGTGAATAAGGCAGGGAGAAAAGGG\n-GGTAAAATTAGGGAATTTAGTAGACTGTCTTAAGTCTTAACTTGAAACTTCTTCAAGAAAGAGAAGATGG\n-TCAGTTGTGGTTCATCAGTAAACTAAGACCTTTGAAACATTTTGTGATAGTCATTTTGATAGCATTTACG\n-TTTATCTTGGATAAAAGTCTTCAAGTCAGCCTTTATGGAAATTATAGTGTCCTGCCCTTCTCCAGCTCTC\n-CTAAGGTTAGTGTTGGCTACACCATTAGGAATAAAAAACCTGAAGACAAAAGGGAAAAGATACAAAAGTT\n-GTATGGAGAGGATAAAGGAAGGATCATTTTTCCTTTGGACTTGGAAAAAAATACATTTAGGTCTTAGATG\n-TTAAAGCTGCCTTTTAGATTTATGAAGGAAAATTTAGGAAAACAGCCTTGAAACCTCATGGGATTTGGAT\n-GGTAACCAAGAGGCAAGGCCTGGAGGTGAGAGTGAGCAGAGCAAGTTATTGGGGAAATCAGGAGATAGCC\n-TGAACTCATTCTTCTAGAGAGTCCTGTAAGTGGTTATGATGATAATCATTGTAATAAAGGTAGGGAATAT\n-AACGTGACTGACTACTTCAAACAGTTCATTTTCTTGGCTCTTAGTACCCCATACTCTCCTAATTGCCTTC\n-CTTCCTCCCAGGTTGGTTATTCTTTACCTCCTTCGGTTAAAGTCCACCAGGCTTTTGTCCTCAGATCTCT\n-CTCTCCAGAAAAGAGAGACGCCCTAGATGATTTCTTCTAGTTCTGGGGGCTTAAATGTCATTGAGATGGT\n-GATAACTCCCAGATTCACTTCTGTAGCCTGGACCTCTCTCTAGAAGTATAGACTTGGCTACCCAGCTGCC\n-AACTGAACTCTACTTGAAGGCCACAGAAGCATCTCAAACTCAACATGTCCTAAACATAACTATTGTTTTT\n-TCCCTTCCTGACCACCCAGAGTGGCTCCTCCTTTATTTTTATCAATTCTTTTAGTTGCCTAGACCAAAAA\n-TATTGGAGTCATTCTTACCTTCTCCGTTTTTCTCATAGGCCACATATATCAATCAGTAAGTCTTGCCATC\n-TTTGCCTTCACAATATATCCTGAATCAGTTACTTTTTGCCATTTCTACTCTAGTCAAGATAAGTACTGCA\n-ATAGCCTCCTGTCTCTCTGCTTTTGCCCTTGTTTCCATGCAGTAGCCAGTCATATTTTAGAAATATACAT\n-CAGGGCTGGGTGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCACGAG\n-GTCAAGAGTTGGAGACCAGCCTGGCCAACGTGGTGAAACCCCGTCTCTACTAAAAATACAGAAATTAGCC\n-GGGCATGGTGGTGCACGCCCATAGTCCCAGCTACTCAGGAAGCCGAGGCAGGAGGATCGCTTGAACCTGG\n-GAGGCGAAGTTTGCAGTGAGCTGAGATCGTGCCACTGCACTCTAGCCTGCTGGGCGACAGAGTGAGACTC\n-TGTCTCAAAGAAAAAAAAGAAATATAAATCAGATTATGTCACCCCTTTGCAATCAGATCATGTCACCCCT\n-CTGCTTAAAATTCTTCACTGGTTTCCTGTCACATTTATTTCATTTTAATGTAATTTTAAATTTTTTTTGT\n-AGTCAGAGTCAGAGCCTCTGTCGCCCAGGCTGGAGTGCAGTGGCATGATCTAGTCACACTTGCAGCCTCT\n-GCCTCCCAGGTTCAAGCTGTTCTCGTGTCTCAGCCTCCCAAATAGCTGGGACTACAGGTGCGTGCTACCA\n-CACCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTTGCCATGTTGGCCAGGCTGGTATCGAACTC\n-CTGAGCTCAAGCAATATGTCCACCTAGGCCTCCCAAAGTGCTAGGATTACAGGTGTGAACCACTGCGACC\n-AGTCCTTATCACTTTTAGAATAAAACTAAAAATCCTCACTTTGGCCACACAGCCTCACAGAATTTGGCCT\n-CTGGCTAGCTATCTGATTTCACATTTGATCATTGTTTGCCCACCTGGCTATACTGCTGGTCTTGCTGTTC\n-CTTAAATTTCATTCAGATTCCTGCTCAGATATCTCCTCAGAGGTGGCAGCTTGTTTGCTTTTATCTAAAA\n-TAGCCACTTCTACCACTTTCACTGTGATCTTTTATCTCCTAACCCGGCTTTATTTTTCTTTCCAACATTA\n-TGCTATTTGTATTAGTTAATTGTCTCATGCTGTCATTAGAATGTAAGCTCCATGTAGGCAGGGACTTGTT\n-TTCACTAGGTATCTATAGGTCATGGTAGACATGCAAGTATTTGTTAAATGAAAGAATATTTTGTACATTT\n-ACTTTATGCTAGGCCTTGAGCCAAAATGTGAGAATTAAATGACAGTTCTGTATAGTTAGGCACTATTATT\n-CAGCAGAACTCAAGCGCAGAGCATCAGACTCAGAGCATCTAGCGACTCAT\n' 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| diff -r 30fc9f2bcbe4 -r 1d4f065fa0ef test-data/genome.fa.gz |
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| Binary file test-data/genome.fa.gz has changed |