| Previous changeset 0:51fd3136069d (2018-06-11) Next changeset 2:aa39b19ca11e (2018-08-17) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a |
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modified:
racon.xml |
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added:
test-data/consensus_result3.fasta test-data/sample_overlaps.paf |
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| diff -r 51fd3136069d -r 4df02149a270 racon.xml --- a/racon.xml Mon Jun 11 16:47:50 2018 -0400 +++ b/racon.xml Thu Jul 19 07:43:14 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="racon" name="Racon" version="1.3.1"> +<tool id="racon" name="Racon" version="1.3.1.1"> <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description> <macros> <import>macros.xml</import> @@ -7,12 +7,20 @@ <version_command>racon --version</version_command> <command detect_errors="exit_code"><![CDATA[ ln -s '$reads' reads.${reads.ext} && - ln -s '$overlaps' overlaps.${overlaps.ext} && + #if $overlaps.ext == 'sam': + ln -s '$overlaps' overlaps.${overlaps.ext} && + #else: + ln -s '$overlaps' overlaps.paf && + #end if ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && racon - reads.${reads.ext} - overlaps.${overlaps.ext} + reads.${reads.ext} + #if $overlaps.ext == 'sam': + overlaps.${overlaps.ext} + #else: + overlaps.paf + #end if corrected_reads.${corrected_reads.ext} -t \${GALAXY_SLOTS:-4} $u @@ -27,7 +35,7 @@ ]]></command> <inputs> <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/> - <param type="data" name="overlaps" format="sam" label="Overlaps"/> + <param type="data" name="overlaps" format="sam,interval" label="Overlaps"/> <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" /> @@ -54,6 +62,12 @@ <param name="e" value="0.2"/> <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/> </test> + <test> + <param name="reads" ftype="fasta" value="sample_reads.fasta"/> + <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/> + <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/> + <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/> + </test> </tests> <help><![CDATA[ |
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| diff -r 51fd3136069d -r 4df02149a270 test-data/consensus_result3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/consensus_result3.fasta Thu Jul 19 07:43:14 2018 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>utg000001l LN:i:48021 RC:i:170 XC:f:1.000000\n+ACAACGTGCGTGGAGGCCATCAAACCACGTCAAATAATCAATTATGACGCAGGTATCGTATTAATTGATCTGCATCAACTTAACGTAAAAACAACTTCAGACAATACAAATCAGCGACACTGAATACGGGGCAACCTCATGTCAACGAAGAACAGAACCCGCAGAACAACAACCCGCAACATCCGCTTTTCTAACCAAATGATTGAACAAATTAACATCGCTCTTGAGCAAAAGGGTCGGGGAATTCTCAGCCTGGGTCATTGAAGCCTGCCGTCGGAGACTAACGTCAGAAAGAGAGCATATACATCAATTAAAGTGATGAAGAATGAACATCCCGCGTTCTTCCCTCCGAACAGGACGATATTGTAAATTCACTTAATTACGAGGGCATTGCAGTAATTGAGTTGCAGTTTTACCACTTTCCTGACAGTGACAGACTGCGTGTTGGCTCTGTCACAGACTAAATAGTTTGAATGATTAGCAGTTATGGTGATCAGTCAACCACCAGGGAATAATCCTTCATATTATTATCGTGCTTCACCAACGCTGCCTCAATTGCTCTGAATGCTTCCAGAGACACCTTATGTTCTATACATGCAATTACAACATCAGGGTAACTCATAGAAATGGTGCTATTAAGCATATTTTTACACGAATCAGATCCACGGAGGGATCATCAGCAGATTGTTCTTTATTCATTTTGTCGCTCCATGCGCTTGCTCTTCATCTAGCGGTTAAAATATTACTTCAAATCTTTCTGTATGAAGATTTGAGCACGTTGGCCTTACATACATCTGTCGGTTGTATTTCCCTCCAGAATGCCAGCAGGACCGCACTTTGTTACGCAACCAATACTATTAAGTGAAAACATTCCTAATATTTGACATAAATCATCAACAAAACACAAGGAGGTCAGACCAGATTGAAACGATAAAACGATAATGCAAACTACGCGCCCTCGTATCACATGGAAGGTTTTACCAATGGCTCAGGTTGCCATTTTAAAGAAATATTCGATCAAGTGCGAAAAGATTTAGACTGTGAATTGTTTTATTCTGAACTAAACGTCACAACGTCTCACATTATATTTACTATCTAGCCACAGATAATATTCACATCGTGTTAGAAAACGATAACACCGTGTTAATAAAAGGACTTAAAAGGTTGTAAATGTTAAATTCTCAAGAAACACGCATCTTATAGAAACGTCCTATGATAGGTTGAAATCAAGAGAAATCACATTTCAGCAATACAGGGAAAATCTTGCTAAAGCAGGAGTTTTCCGATGGTTACAAATATCCATGAACATAAAGATATTACTATACCTTTGATAATTCATTACTATTTACTGAGAGCATTCAGAACACTACACAAATCTTTCCACGCTAAATCATAACGTCCGGTTTCTTCCGTGTCAGCACCGGGGCGTTGGCATAATGCAATACGTGTACGCGCTAAACCCTGTGTGCATCGTTTTAATTATTCCCGGACACTCCCGCAGAGAAGTTCCCCGTCAGGGCTGTGGACATAGTTAATCCGGGAATACAATGACGATTCATCGCACCTGACATACATTAATAAATATTAACAATATGAAATTTCAACTCATTGTTTAGGGTTTGTTTAATTTTCTACACATACGATTCTGCGAACTTCAAAAAGCATCGGGAATAACACCATGAAAAATGCTACTCGCTACTGCGCTGGCCCTGCTTATTACAGGATGTGCTCAACAGACGTTTACTGTTCAAACAAACCGGCAGCAGCAGTAGCACCAAAGGAAACCATCACCCATCATTTCTTCGTTCGTTTCTGGAATTGGGCAGAAGAAAACTGTCGATGCAGCCAAATTTGTGGCGGCGCAGAAAATGTTGTTAAAACAGAAACCCAGCAAACATTCGTAAATGGATTGCTCGGTTTTATTACTTTAGGCATTTATACTCCGCTGGAAGCGCGTGTATTGCTCACAATAATTGCATGAGTTGCCCATCGATATGGGCAACTCTATCTGCACTGCTCATTTAATACTTCTGGGTTCCTTCCAGTTGTTTTGCATAGTGATCAGCCTCTCTCTGAGGGTGAAATAATCCCGTTCAGCTCTGTCTGCCAGTCGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACTGCTTTGATGTGCAACCGACGACGACCAGCGGCAACATCATCACGCAGAGCATCATTTTCAGCTTTAGCATCAGCTAACTCCTTCGTGTATTTTGCATCGGAGCGCAGCAACATCACGCTGACGCATCTGCATGTCAGTAATTGCCGCGTTCGCCAGCTTCGATTCAGTTCTCTGGCATTTTGTCGCGCTGGGCTTTGTAGGTAATGGCGTTATCACGGTAATGATTAACAGCCCATGACAGGCAGACGATGATGCAGATAACCAGAGCGGGAGATAATCGCGGTGACTCTGCTCATACATCAATCTCTCTGACCGTTCCGCCCGCTTCTTTGAATTTGCAATCAGGCTGTCAGCCTTATGCTCGAACTGACCAGACCAGCGCCCGGCAGTGAAGCCCAGATATTGCTGCAACGGTCGATTGCCTGACGGATATCACCACGATCAATCATAGGTAAAGCGCCACGCTCCTTAATCTGCTGCAATGCCACAGCGTCCTGACTTTCGGAGAGAAGTCTTTCAGGCCAAGCTGCTTGCGGTAGGCATCCCACCAACGGGAAAGAAGCTGGTAGCGTCCGGCGCCTGTTGATTTGAGTTTTGGGTTTAGCGTGACAAGTTTGCGAGGGATCGGAGTACGCGATAATCAGTAAATAGCTCTCCGCCTACAATGACGTCATAACCATGATTTCTGGTTTTCTGACGTCCGTTATCAGTTCCCTCCGACCACGCCAGCATATCGAGGAACGCCTTACGTTGATTATTGATTTCTACCATCTTCTACTCCGGCTTTTAGCAGCGAAGCGTTTGATAAGCGAACCAATCGAGTCAGTACCGATGTAGCCGATAAACACGCTCGTTATAAGCGAGATTGCTACTTAGTCCGGCGAAGTCGAGAAGGTCACGAATGAACTAGGCGATAATGGCGCACATCGTTGCGTCGATTACTGTTTTGTAAACGCACCGCCATTATATCTGCCGCGAAGGTACGCCATTGCAAACGCAAGGATTGCCCCGATGCCTTGTTCCTTTGCCGCGAGAATGGCGGCCAACAGGTCATGTTTTCTGGCATCTTCATGTCTTACCCCCAATAAGGGGATTTGCTCTATTTAATTAGGAATAAGGTCGATTACTGATAGAACAAATCCAGGCTACTGTGTTTAGTAATCAGATTTGTTCGTGACCGATATGCACGGGCAAAACGGCAGGAGGAGTGTTAGCGCGACCTCCTGCCCGCCCTTTCACGAAGGTCATGTGTAAAAGGCCGCAGCGTAACTATTACTAATGAATTCAGAACAGACAGTGGCTACGGCTCAGTTTGGGTTGTGCTGTTGCTGGGCGGCGATGACGCCTGTACGCATTTGGTGATCCGGTTCTGCTTCCGGTATTCGCTTAATTCATTCAGCACAACGGAAAGAGCACGCACTGGCTAACCAGGCGCCGACTCTTCACGATTATCGACTCAATGCTCTTACCTGTTGTGCAGATATAAAAATCCCGAAACCGTTATGCAGGCTCTAACTATTACCTGCGAACTGTTTCGGGATTGCATTTTGCAGACCTCTGCCTGCGATGGTTGGAGTTCCAGACGATACGTCGAAGTACCAACTAGGCGGAATCGGTAGTAAGCGCCGCCTCTTTCATCTCACTACACAACGAGCGAATTAACCCATCGTTGAGTCAAATTTACCCAATTTTATTCAATAAGTCAATATCATGCCGTTAATATGTTGCCATCCGTGGCAATCATGCTGCTAACGTGTGACCG'..b'GAATTTTCGCCGCCCCATAAAATGACGCCCACGACTCGTTCGCACTGGCCCGTGCCGTGGAGTAGCTCATCTGGGCGTAATTCCGGGAAAGCTGCTCATACGAGACACCCAGCCCGGCAGCGATATACCGCAGCAGTGACTGCTCAAACACGGAGTAGCCGTTATCCGTATCCTGAGCCGTCTGCAGGTTCAGTGAGAGTACCGGCATCAGGTGCGGTACTTTTGCGCCTCCAGCCGGACCGGCGCTGCTGCGGCGTAATACGCGGCAATTTCACCAATCCAGCCGGTCAGCCTTTCCCGCTGCTCCTGACTGTTCGCGCCCAGAATAAAATCCATCGCTGACTGCGTATCCAGCTCACTCTCAATGGTGGCGGCATACATCGCCTTCACAATGGCGCTCTGCAGCTGCGTGTTTCTGCAGCGTGTCGAGCATCTTCATCTGCTCCATCACGCTGTAAAAACATTTGCACCGCGAGTCTGCCCGTCCTCCACGGTTCAAAACGTGAATGAACGAGGAGGCGCCCGCCGGGTAACTCACGGGGTATCCATGTCCATTTCTGCGGCATCCAGCCAGGATACCCGTCCTCGCTGACGTAATATCCCCAGCGCCGCACCGCTGTCATTAATCTGCACACCGGCACGGCAGTTCCGGCTGTCGCCGGTATTGTTCGGGTTGCTGATGCGCTTCGGGCTGACCATCCGGAAGAACTGTGTTTAGAAAAGCCGCGACGAACTGGTATCCCAGGCCTGAACGAACAGTTCACCGTTAAAGGCGTGCATGGCCACACCTTCCCGAATCATCATGGTAAACGTGCGTTTTCGCTCAACGTCAATGCAGCAGCAGCAGTCATCCTCGGCAAACTCTTTCCATGCCGCTTCAACCTCGCGGGAAAGGCACGGGCTTCTTCCTCCCCGATGCCCAGATAGCGCCAGCTTGGGCGATGACTGAGCCGGAAAAGACCCGACGATATGATCCTGATGCAGCTGGATGGCGTTGGCGGCATAGCCGTTATTTGCGTACCAGATCGTCTGCGCGGCATTGCCACGGGTAAAGTTGGGCAACAGGGCTGCATCCACACTTTCACTCGGTGGGTTCCACGACCGCAACTGCCCTCCAAATCCGCTGCCACCGCCGCGTGATAACCGGCATATTCGCGGGGCAGCGATGTCATGCCGTCCGGCCCCAGAAGGGTGGGAATGGTGGGCGTTTTCATACATAAATCCTGCAGGTCTCTCCCTGCGTCGCTGTGTCATGCCGGTCTGCACTTCCAGCTCTGCAATATATTTTTCAGGTCAGACACGGAAGTGGCCGTAAACTCCACCCTTCGTCCGTCTTTCTGTACTGTTGCCACCCGTTTACCTGTCATCAGGTCATGCAGTGCCGCACGGGCAGCGGCAAGTTCTTCCTGTCGCGTCATTCATCCTCTCCGGATAAGGCACGGCGTAATCTGCCAGTGTTTTCTTGTTGGTTGCTGCACCATCCTCTTCCTGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTGCTGTCCACAGTATTTTCCTGCCATCCACCCATTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGGTCAGATCAAAATATCCGGGTTATTTCGGGAATGAACGGCACCGGGAAGCGGTTCATCCCCTTCCGGCGTCAGTGTGAAGCGGTTTATAAATCTGCTCTTCGCGGTATCCGTACCGATTTCGGTAAGGTAAACCCCGTTTTGTTTCGCTTACGTGGCATGCTGGCCACCGGCTTTCCGTAGACGGATGCCCCTTTAATGGGGATCACCCGGAACAGCCCATGTTTTCGAGCGTTCATACACAATGGTCGGGTCAATCCCGCCAGTATCCCAGCAGATACGGGATATCGACATTTCTGCACCATTCGGCGGGTATAGGTTTTATTGATGGCCTCATCCACGCAGCAGCGTCTGTTCATCGTCGTGGCGGCCCATAATAATCTGCCGGTCAATCAGCCAGCTTTCCTCACCCGGCCCCCATCCCCATACGCGCATTTCGTAGCGGTCCAGCTGGGAGTCGATACCGGCGGTCAGGTAAGCCACACGGTCAGGAACGGGCGCTGCGCTGAATAATGCTCTTTCCGCTCTGCCATCACTTCAGCATCCGGACGTTCGCCAATTTTCGCCTCCCACGTCTCACGAGCGTGGTGTTTACGAAGGTTTTACGTTTTCCCGTATCCCCTTCGTTTTCATCCAGTCTTTGACAATCTTAAGAGGTGGTGAACGGGCTGTACGCTGTCCAGATGTGAAAGGTCACACTGTCAGTGGCTCAAATCTTTCACCGGATGACGAAAACCAGAGAATGCCATCACGGGTCCAGATCCCGGTCTTTCGCAGAGATAACGGGCATCAGTAAGAGTCCAGCTCCTGCTGGCGGATGACGCAGGCATTATGCTCGCAGAGATAAAACACGCTGGAGGGATCATCAGCGTCCATTTGAGGCCAAACGGCGTCTCTTTGTCGCCAAATTTAAGATACTGCTCCTCCCCCGCAATGCGGGCAGGCAACATGAAAACGCATAAAATGCGGGGATTCACTGGCTGCACGCTCTCAATCTGACAGGTGCCTCTCACTTTGGCGTGGAGCCACGGATGGACTTTACAGACCGAGCCTTCAATACGCTTGTTACCCAGGAACGTCGGAGAGCCTTCCTGTTCAATATCATCATCAAAAGCAGCAAGTTCATCATAACCCGCCACATCCACCGACGACTTTCACGGTAGTTTTGCCGCTTTACCGCCCAGGCAGCACCAGAAGCCACGCCCATTAGTGAACGCTTCATGGTGAGCGTGTTATCCCGGTGCTTTTGCCATACCACGGGGCCAGCGCCAGCAGCGACGGAATATCACGAATAGTCGGCTCAACGTGGGTTTTCATAAAGTTCTCGGCATCACCATCCGTCGGCAACCAGATAAGGGTGTTGCGCTGCTTATGCTCTATAAAGTAGGCATAAACACCCAGCAGCATTTTGGAATAACCGACACGGGCAGACTTCACCACATTCACCTCACGGATGTAGTCGCTGCCATCGCATTCATGATGGCCCGCTGAAAGGGCAGTGTTTCCCAGCGCCCTTCCTGGTATGCGGATTCTTTCGGGAGATAGTAATTAGCATCCGCCCATTCAACGGCGGTCTGTGGCTCCGGCCTGAACAGGAGCGCGAAGCCCGGCGCGGACAAAATGCCGCAGCCTGTTAACCTGACTGTTCGATATATTCACTGAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGAGCCGTCGAGAATACTGGCAATTTCACCTGCGATTGACGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAACCTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTCGGCATACCATTTTATGACGGCGGCAGAGTCATAAAGCACCTCATTACCCTGCCACCGCCTCGCAGAACGGGCATCCCTGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTGTTGACTTCCATTGTTCATTCCACGGACAAAACAGAGAAAGGAACGACAGAGGCCAAAGCTCGCTTTCATAGACCCTGTCGTTTCCTTCTTTCAGAGGGTATTTTAAATAAAAACATTAAGTTATGACGAAGAAGAACGGAAACGCCTTAAACCGGAAAATTTTCA\n' |
| b |
| diff -r 51fd3136069d -r 4df02149a270 test-data/sample_overlaps.paf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_overlaps.paf Thu Jul 19 07:43:14 2018 -0400 |
| b |
| b'@@ -0,0 +1,172 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