| Previous changeset 4:dc684e37f668 (2016-05-12) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit a5df655e2dae7ee5863305847b923716b2cdf661 |
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modified:
README oases_optimiser.xml |
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removed:
test-data/output.fa tool_dependencies.xml |
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| diff -r dc684e37f668 -r 68ed36eed6c5 README --- a/README Thu May 12 10:45:03 2016 -0400 +++ b/README Sun Apr 16 18:01:04 2017 -0400 |
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| @@ -1,3 +1,9 @@ +# 15/04/2017 +The tool now uses bioconda dependencies + <requirement type="package" version="0.2.09">oases</requirement> + <requirement type="package" version="1.2.10">velvet</requirement> +As the output is not deterministic, test search for line matching oases locus ranging in 1-25 + #Created 28/11/2014 #Christophe Antoniewski, CNRS/University Pierre et Marie Curie, drosofff@gmail.com # inspired from the oases wrapper developped by Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter |
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| diff -r dc684e37f668 -r 68ed36eed6c5 oases_optimiser.xml --- a/oases_optimiser.xml Thu May 12 10:45:03 2016 -0400 +++ b/oases_optimiser.xml Sun Apr 16 18:01:04 2017 -0400 |
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| @@ -1,7 +1,8 @@ -<tool id="oasesoptimiserv" name="Oases_optimiser" version="1.1.5"> +<tool id="oasesoptimiserv" name="Oases_optimiser" version="1.2.1"> <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description> <requirements> - <requirement type="package" version="0.2.08_7a32460a60929b510037952ae815bb6e29b68123">oases</requirement> + <requirement type="package" version="0.2.09">oases</requirement> + <requirement type="package" version="1.2.10">velvet</requirement> </requirements> <command><![CDATA[ python "$__tool_directory__"/oases_optimiser.py "$start_hash_length" "$end_hash_length" @@ -49,7 +50,12 @@ <param name="input" value="input.fa" ftype="fasta"/> <param name="start_hash_length" value="15" /> <param name="end_hash_length" value="35" /> - <output name="transcripts" file="output.fa"/> + <output name="transcripts"> + <assert_contents> + <has_line_matching expression=">Locus_1_Transcript_1/1_Confidence_.+" /> + <has_line_matching expression=">Locus_25_Transcript_1/1_Confidence_.+" /> + </assert_contents> + </output> </test> </tests> <help> |
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| diff -r dc684e37f668 -r 68ed36eed6c5 test-data/output.fa --- a/test-data/output.fa Thu May 12 10:45:03 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,237 +0,0 @@\n->Locus_1_Transcript_1/1_Confidence_0.000_Length_342\n-TCTTAAAAATAGAGTTATCCTGAAGTTGCAACAGGCGAAGATGGGAAATAGAATCTTGAG\n-TTTTTCAAGTTCAAAATTAAAGGACCAACCCATCAAAATAGCGCAAGCGAAGAGTGGAAG\n-GACGAGAGTATTCCATTGTATCCCAGTGGATTTAATCTTGTTTTCGGGAGCGCTATACGG\n-CCCGTACAAAGAAGCATACACAAAGGCTGGACTGAAATGCTATCATGCTGTAGGAATAGA\n-TCCGAAATCAGTTGGTTGGCAACAGTTGGCTACGTATATGACGAAGCATCCTAATTATTT\n-TGATGCTGATTATAAGAACTACGATAAGTACTTGCATAGGCA\n->Locus_2_Transcript_1/1_Confidence_0.000_Length_1211\n-GGTCTATGACCATTCTGCGGTTCCTGTAGCGCCAGTCGTCGAAACACAAGCAGAACAGCC\n-GGAAGTTCCAGTATCATCAGTGGCAACGCGAAAGAACGATACGGGACATCTGGCAACAAA\n-GTGGTATGATTTTGCCAAAATTAGTCTGTCAAACCCAGCTAACATGAATTGGACCACACT\n-AACCATAGACCCGTACAACAATGTTACATTGTCTAGGGATGGTGAGTCGATGGTTCTACC\n-GTGGAGGCGAAATGTTTGGACAACCGGATCAAAAAGTATTGGATACATCCGAACAATGGT\n-TGCACAGATTAACATACCACGTCCGCCGCAGATCAGTGGAGTGCTCGAAGTTAAAGATTC\n-AATCAATAATTCAAGTATTTCACTGGTTGAATTTGGAGGAAAAGTGGAAATCCCAATTAT\n-TCCGAAGGTTATGAACGGACTAGCAACAACTGCTAGTTTGCCAAGGCATAGACTAAACCC\n-GTGGATGAGAACCGCCGAAAGTAAGGTTGAATTGCAATATCGAATTATTGCTTTTAATCG\n-AACTAGCGACATTGCTGACCTCAACGTTAGCGTTTTGTTGCGACCTGGCGATTCGCAATT\n-CCAATTGCCGATGAAACCTGACAATAATGTGGATACACGTCATTTTGAGCTTGTTGAAGC\n-TTTGATGTACCACTACGATAGCCTCCGAATTCGAGGAGAAGAACAGAGTCTGCCAGAAAA\n-TGCACCTAATGCAGTTTCAAACCCTCAGCAGTTCATCACACCCGCAACCGCTCTAAGTGC\n-CGAAGAATATAACGTGCACGAGGCGTTGGGTGAGAGTGAGGAATTGGAGCTGGATGAGTT\n-TCCAGTTCTGGTGTTTAAGGGAAATGTTCCCGTTGACTCAGTGACGTCCATTCCTTTGGA\n-CCTCGCAACCATATACGACTTCGCTTGGGACGGAGAACAGAATGCAATTTCTCAGAAATT\n-TCAGCGTTTTGCTCATTTGATACCGAAAAGCGCAGGTGGTTTTGGCCCAGTGATTGGTAA\n-TTATACTATCACGGCTAACCTCCCCACCGGTGTAGCAGGTCGTATTCTGCACAATTGTCT\n-CCCAGGAGATTGTGTAGATCTAGCAGTATCGAGAATCTTTGGTTTGAAGAGCCTTCTTGG\n-TATTGCAGGAACAGCAGTTTCAGCTATTGGTGGCCCACTCCTTAACGGTTTGGTTAACAC\n-TGCAGCGCCTA\n->Locus_3_Transcript_1/1_Confidence_0.000_Length_757\n-CGAATTAAGTCGACTTGGTGATTGTGGAAGTCCAATTGTCTTGGCGTCAGGAAAGAAGGC\n-AGGAAAACTGATAGGTTTTCACGGTTATCACTCTCCAAATCTACAAACGTGGTACGGAGC\n-AATGTTGACTGTTGAGGACTTGGGAATCATCAACGGCGTAGAAGAACATTTTGATGACCC\n-ATGGGCCAAACTTATTACACAAGGACTACCTGTCGATTTGCCAATTGGACCAGAAGTTGA\n-GTATGTCGGTAATCTAATAAGACCTAGTTTACCTGTGACAAATGACTCACTAGACCATTG\n-GCACAAATCACCATTTGCTGATCAATTTGAAGAACAATTAGCACCTGGTCGATTGAATCC\n-GTATGATTCATATATTGAAGGAGATTTGCCAACTAATCTTGAGGGCCGAAAAAGTTTAAT\n-CTTAGGCCCGAATAGTGAAATGGCAAAAACTCTTCCAGAATTGGATCAAGGAATTATCGA\n-CTGGATTGTAGATCAGTTGGTGGTGGAACAAGTCGCAACTTTCAAAGCAGAAAACCTTTT\n-AACGAAAGTTAGTGACGATATTGACGAAATGCTTGACTATGCCCTGAATGGAAATGTAGA\n-TAATACGTATGTTAGGGGTATGGAAGTCAACAAAGCATCAGGATTACCTTGGAGTCTTTC\n-AGGTAGTCCGAAAAAGAGTGACTTTATCGATGTAGATGAAGCTACTGGAGTCAGATCGTT\n-TAAGGTTAATGCTAATGGAGACGCTCTTAAAAATAGA\n->Locus_4_Transcript_1/1_Confidence_0.000_Length_131\n-TCTCAATTTAGAGAGTTAGTAGACAAGTTAGAAACTGGCATTCTATTCCATGAAATAAAA\n-TCGGTCACAAATGGAATTAGATGGTTAGGAGGAGCAGGGAACAATGGACACGTTGGAGAA\n-AGAGTAAGAGT\n->Locus_5_Transcript_1/1_Confidence_0.000_Length_588\n-GGTGCACCGCAAGCATCTACGCAGGCGACCGATACTATGGACGTGCTGGTGAATAAGCAT\n-TTAGTTAAAGTTCATTGTCTGAGTTATGAAAATTTGAATAATTTGGCTTTGAATGGAACA\n-CAAGTGTTTGCTCTAGCATCCGACAATATATTGATCGTACCTGCACATGCAGCCAGACAG\n-AACAAGTGGATCCGGTTTAGTCGCGCAACACAGACTGGTCATTATGGAATAGCGAAAGTC\n-GATGAACGTAGAATTGATTTTACACGTGACATCGCTATAGCCGTTATTTTGACCAGAGCT\n-GAAGCAGAACAAAAATTGTGCGAACTAGGTCACTCGATCCAGTTAACGAATATTAGTAAA\n-GAGAAATTCCACTTCCCTCTTATTACGAAATATTTGTTAACCGCTGACCAGTCAGAAGTA\n-GAATGGATGAATTGTACGACCCTACATTATTTTGCAAAGAATAGAACCGTGGGGTTAGGA\n-AGAACGACATCATTCCAAGTTTCCGAATTTTTATGTGGAAACGAGTACATATCCAAAAAA\n-CTGGTCGCATGCGCGCAAGGACTCCAGTCAAGTGTCGAATTAAGTCGA\n->Locus_6_Transcript_1/1_Confidence_0.000_Length_365\n-ATTCAAATATGATTAACAATCAAACAAACAAAAAGGGACCACAACTAGAGAGAGTACATT\n-TTGGTAGTGCGCAAGTTGTGGGAAAAAGTACCAAACGACGACAACGCGGAACCAAACTTG\n-ACATTGAATATACTGTTAAAAGGAACGAAGCACCAAAAGAGCAGAAATTCTTAGTTTCAG\n-AAATTTTTGATGAAAAGTTGGATAAACAAATAAAATATGAGAAGAAGCAAAATCATACTT\n-TTATTAAACCGAAATTAAATTTAGTTACTAGAGAAGAACAACATGTGACTAAGAAGGTTT\n-TAAGAGGTAAAGAACGAGCTGCAACTCATGCTTTTATGAAGGAGATGGTTGAATCTAACA\n-AGATA\n->Locus_7_Transcript_1/1_Confidence_0.000_Length_137\n-ATATGACATGCCCCTACGCGTTATCGCTGGCCTGTCAACCCTTGCCAAAACAACTGAAGA\n-AGACGACAACACCTCAACTGGAATAGTAGTTA'..b'>Locus_19_Transcript_1/1_Confidence_0.000_Length_570\n-GCAAACCTGATTTTCCGAGGGGCTACCCATAGTTATAAAAACTATTGGTTCAGCCAGAGT\n-AACCCTTTCGGAAACGCAAAAGCTTAAAAAACCTGTTTATCGAGATTCCACTACTCCCCG\n-CGTGGGGAGTCGTTTGCACAGATATTCTCAATAAATGTTAATTTTTCTCCTATAAACTAT\n-AGGTATTAACTTTCAGGAAAAGTTGCAATTGCTAGCACTACGAACCCACACCCAGTGCGG\n-GCTCCAAAACATCATCACACCGTCCTTTATAATCTTCTGCTAGAAAATTATAGCGACCAT\n-CCTCATATTTAATGTGATTTTTTAACCATACGCGCAAACCAATTTTAAAAATTAGTTTCT\n-GAGACGCGCACATGGCGAGTTTTGGATTTAATCTACTGCCTCACGGAAGGGAAAACAGTT\n-TCTGCTACGTTTCGTTCCGTCCTGCGTTTACTTTCACCTAATACGATTTTGCGGGTCGTA\n-GTAGGTAGCAGACCGGTGTCTGTTCGCGAAAATTCTTCCGTGGTCTCCCCACTCGAGTTT\n-GTACTCAAGTAGCGTTTTACTCTCTCTATT\n->Locus_20_Transcript_1/1_Confidence_0.000_Length_193\n-AACTACTTTAGCTAAACCGTCAAGTTGCAGTTTTTGTTGATCGAGCTGGTTTTTTACTGC\n-TGTTACTGAGGATTGAATTGACTTAATCTCAGTAACCTCGTTCTCGTCTAAAACGGCGAA\n-AAGAGTGGTGTTCTGATCAAAGATCTCCTCTTTTAATGCCATAATAACGATTACAGAATT\n-TTTGGAAAGTAAA\n->Locus_21_Transcript_1/1_Confidence_0.000_Length_224\n-TTTCCAGCTCGTATTCAACAATACTGCTAATGCTCCATTCAAGGTTCTGTTTGTACCACA\n-TTTTAGCTTTTGACAAAGTTCATTGTAGTAATCTTCACCCCAAAGAGCTGCTTCGATCAA\n-CTGTTCTTGCACAAGATTTACCCACACAGTTATCTGATCTTCGCGGATATCAGTCCATAC\n-AAACGGTCCCTCAATAGATCGTTGTAGCAATGGAGCTAAAACCA\n->Locus_22_Transcript_1/1_Confidence_0.000_Length_211\n-AGAAAAAGTAAATATTCTTTGGAACCTCATTAGGCTCCAACCTCAACATGAGGTGGAGAA\n-TTTTAAGGTTTACTTAGAAGATTTGCAGGCGTCCCCGCCGAAAACTGGGACAATTTGTGC\n-AAAAGTAGTGAATGATATAAAAGCTGAAGTAGCTTCAAGTTATAGGCAATTTAACAATTA\n-CTACACTCGTTTAACAAAAGATGGTATGCAC\n->Locus_23_Transcript_1/1_Confidence_0.000_Length_245\n-TGTTAATTGAAGCTTTCATTAATTCTTTGTTGCAAAATCTAGGTATCATGATGTCTTTCC\n-GTGACCTAGTGGCGAGCCCATGGATATTGCTAGTAATAGCTATACCCTTGTGTGCATTTG\n-CCAGTTCAGCGTCTATGGTTAGGGAGATGCTTTTCCGTCATAAAATTACAGAAAATATTT\n-TAAAAGGAACAGGAGTAGAAGAATTGTTTAATCCATTCGGGATAATTATTAAATATTTCC\n-TTTAT\n->Locus_24_Transcript_1/1_Confidence_0.000_Length_577\n-AAAAATTGAAGTTTACACTTGGCAAAGAACAAGCTGAAGGGGATAGTATCGAACATGTTA\n-AAGAATTTGACGGTGATGTTAAGTTCGAAACAATTGAGAAACTGTTTGATCATATTGATG\n-AACACCCTAACCTTAACATAGTAGGCTTGAATTTGATAGCACCAGAAAACCCAATTGCTA\n-TCTATGCCGCAAGAGAAGAATCGTACGACTTTTCATTCTCCGAACCGCGCCCGCCTCAAT\n-GGAAAAAGGTGGTAACGTTTAAGGAAGACAGTAAACGAATAATCTCTCTACAGTTGCGAG\n-GAGAAGATACTGAAGATAACATCCTCGATGAGATTGAACACGCTATAAAAGTCTCACATG\n-GAATGCCGTATGCTGAATGGATATTCAATGGATGGTTTAAGAAAGAGAGCAACGACAATA\n-TATTATATTGTGTCGAGTTGGACCTGGTGACCGCAAAAACCCAATCAGGCCCAGTTGGAT\n-GGACACGTGCTCAAACGAAGAACCTGAAAGATCTTGAAATTCAGCTAAACAAAGGCAAAC\n-CGATCGATGTTAAATCAGTGGTTTTAGGTGCACCGCA\n->Locus_25_Transcript_1/1_Confidence_0.000_Length_603\n-TGGTCATAGACCAATTCCTGTACAAGTTTACCACCTTCGGCTGTAACTTCATTGTCAGCT\n-TGTTCTTCGCCCGTAATTGGTTTAGTTGGGGGAACGGGCGGCTTTGGCACTGGAACTGGG\n-ATAAAGTTCATGCCTTTTTCATTATAAGCTGACGTATCTGCATGCTTATAGCCTGTGGCT\n-TTAATGTTCGCCATGCAACACCAAACGGTGATGCTGAGTGGGGTATTGACCGTTTCGTTA\n-CTGTTATCTTCGATGGTTTCAATAACAATACTTCCTCCACTCTGTCCGATTCGACCCACT\n-GATGTTTCTACGGTCGATAGATCGTTGCTCCAAGGAACTGAAAGTGCAATGGTTGGAGAT\n-GCACTTGGCTTGAACCGAATTCCTCGTGTTACGGTTGTAGTATCAAATTCAGGAGTGTAG\n-ATCTTCAGATAGATACCTGTTCCCAAAGGTGCTGGAACATGCACTATATAATAAAAATCC\n-GCATGGAAATAATTATATAGTTCTAGCACCGTTTTTTGTTGGTAAGTGAAAACAGGATCT\n-ACCACAAGTCGGGTTCCTACTGCTGGAGCAGAAAAGCGGCGTGGCAAGAAAGCACTAAAC\n-GCA\n->Locus_26_Transcript_1/1_Confidence_0.000_Length_182\n-TAGTTATACTACTACAATTGATAATTGCCTGGCGAACGATATTTATGGTTTGTATGCGTG\n-GGTGAAGACAACCGGCCTAAGATCACTGTGGGATTACCGACAGAATGTCTCGAGCGTCGC\n-GTTTGGTGATGATATTATAAAAAGCGTTAGCGATGAGTATAAAGATAAGTATAATTATTG\n-TA\n->Locus_27_Transcript_1/1_Confidence_0.000_Length_151\n-TATTTACTTTTTCTTCTCCTATAAGCGAGTGATACTTATAGTCCGAGTTTATGACGAGCT\n-GGATCCATTCCCTGTGCAGTTCTTCGTTTATAGGGAATCCATTCTGAGGGTAACTCTTTT\n-TCGGAAATTGGGCTGTATGAGCAATAACTCT\n->Locus_28_Transcript_1/1_Confidence_0.000_Length_215\n-TAAGAGATTCTGTCGTTGTGTTCAACGTGTCTAAGGAATCTTTCGTAGTTTGATCAAGCT\n-CATTTAATGCTGTGGCAAGGGTGTTAATCTGTTTTGCCTGTTGACTTGTTGTTGTGGTTA\n-ATTTATCAACTTCTGAACTCATTTCTACCAATGTTGTATTGATATTAACGAATTGTTCTT\n-CATTTCGAGCTTGATTGTTGTTAACTACTTTAGCT\n->Locus_29_Transcript_1/1_Confidence_0.000_Length_113\n-TCAATTTTTGAAGCTTAGTAGTTGCGATGTTCTTCTGTTTGGCTCGTTTTTCACCTTTAC\n-TCTGCTCTTCCCCAGCTATAGCATATTGGAAAGTTTTCACTATTGTAATAATA\n' 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| diff -r dc684e37f668 -r 68ed36eed6c5 tool_dependencies.xml --- a/tool_dependencies.xml Thu May 12 10:45:03 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="oases" version="0.2.08_7a32460a60929b510037952ae815bb6e29b68123"> - <repository changeset_revision="76e8c94ea259" name="package_ged_oases" owner="drosofff" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |