Galaxy |

Changeset 0:e9c1cdb9f9dc (2017-07-06)

Next changeset 1:f13d0498a199 (2017-09-29)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b

added:
test-data/assembly_test1.fa
test-data/assembly_test2.fa
test-data/onp.fa
test-data/phix_f.fq.gz
test-data/phix_r.fq.gz
unicycler.xml

diff -r 000000000000 -r e9c1cdb9f9dc test-data/assembly_test1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assembly_test1.fa Thu Jul 06 17:07:43 2017 -0400

@@ -0,0 +1,78 @@
+>1 length=5386 depth=1.00x circular=true
+TACGGGGAAGGACGTCAATAGTCACACAGTCCTTGACGGTATAATAACCACCATCATGGCGACCATCCAA
+AGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGAAGAAGACTCAAAGCGAACCAAACAGGCA
+AAAAATTTAGGGTCGGCATCAAAAGCAATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAG
+ATGTATCCATCTGAATGCAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAA
+CGTTGACGATGTAGCTTTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAACC
+AGCTTATCAGAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATTAAACTCCTAAGCA
+GAAAACCTACCGCGCTTCGCTTGGTCAACCCCTCAGCGGCAAAAATTAAAATTTTTACCGCTTCGGCGTT
+ATAACCTCACACTCAATCTTTTATCACGAAGTCATGATTGAATCGCGAGTGGTCGGCAGATTGCGATAAA
+CGGTCACATTAAATTTAACCTGACTATTCCACTGCAACAACTGAACGGACTGGAAACACTGGTCATAATC
+ATGGTGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAAGCCTTCA
+AGAAGGTGATAAGCAGGAGAAACATACGAAGGCGCATAACGATACCACTGACCCTCAGCAATCTTAAACT
+TCTTAGACGAATCACCAGAACGGAAAACATCCTTCATAGAAATTTCACGCGGCGGCAAGTTGCCATACAA
+AACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTC
+GCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAGAAACGCGGCA
+CAGAATGTTTATAGGTCTGTTGAACACGACCAGAAAACTGGCCTAACGACGTTTGGTCAGTTCCATCAAC
+ATCATAGCCAGATGCCCAGAGATTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAGAGGTT
+TTACCTCCAAATGAAGAAATAACATCATGGTAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTATGCA
+AATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAG
+CTCAGTCTCAGGAGGAAGCGGAGCAGTCCAAATGTTTTTGAGATGGCAGCAACGGAAACCATAACGAGCA
+TCATCTTGATTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCATCCACGGCGCTTTAAAATAGTTGT
+TATAGATATTCAAATAACCCTGAAACAAATGCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGCCAAG
+AAAAGCGGCATGGTCAATATAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCATTAACACCATCCTTC
+ATGAACTTAATCCACTGTTCACCATAAACGTGACGATGAGGGACATAAAAAGTAAAAATGTCTACAGTAG
+AGTCAATAGCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTC
+GCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCAGCAAGGAAGCCAAGATGG
+GAAAGGTCATGCGGCATACGCTCGGCGCCAGTTTGAATATTAGACATAATTTATCCTCAAGTAAGGGGCC
+GAAGCCCCTGCAATTAAAATTGTTGACCACCTACATACCAAAGACGAGCGCCTTTACGCTTGCCTTTAGT
+ACCTCGCAACGGCTGCGGACGACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAGACATTACATCACTC
+CTTCTGCACGTAATTTTTGACGCACGTTTTCTTCTGCGTCAGTAAGAACGTCAGTGTTTCCTGCGCGTAC
+ACGCAAGGTAAACGCGAACAATTCAGCGGCTTTAACCGGACGCTCGACGCCATTAATAATGTTTTCCGTA
+AATTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAATGTTGACGGGATGAACATAATAAGCAATGACGG
+CAGCAATAAACTCAACAGGAGCAGGAAAGCGAGGGTATCCTACAAAGTCCAGCGTACCATAAACGCAAGC
+CTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAAAATCGAAA
+TCATCTTCGGTTAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAATAGAGGCCAAAGCGGTCTGGAAAC
+GTACGGATTGTTCAGTAACTTGACTCATGATTTCTTACCTATTAGTGGTTGAACAGCATCGGACTCAGAT
+AGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGTGACTCATATCTAA
+ACCAGTCCTTGACGAACGTGCCAAGCATATTAAGCCACTTCTCCTCATCCAACGCGTCAGTTTTTGACAG
+AATCGTTAGTTGATGGCGAAAGGTCGCAAAGTAAGAGCTTCTCGAGCTGCGCAAGGATAGGTCGAATTTT
+CTCATTTTCCGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTATCAAG
+ATAATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAAACTCTGC
+AGGTTGGATACGCCAATCATTTTTATCGAAGCGCGCATAAATTTGAGCAGATTTGTCGTCACAGGTTGCG
+CCGCCAAAACGTCGGCTACAGTAACTTTTCCCAGCCTCAATCTCATCTCTCTTTTTGCGTTCTGCTTCAA
+TATCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTT
+GTCATTGTGAGCATTTTCATCCCGAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCG
+ACAGCTTGGTTTTTAGTGAGTTGTTCCATTCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATATCTGA
+CTTTTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAAGCGGCTCACCT
+TTAGCATCAACAGGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGAACTGCGATGGGCA
+TACTGTAACCATAAGGCCACGTATTTTGCAAGCTATTTAACTGGCGGCGATTGCGTACCCGACGACCAAA
+ATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCATAAAGTGCACCGCATGGAAATGAAGACGGCCATTA
+GCTGTACCATACTCAGGCACACAAAAATACTGATAGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCT
+CGGCAGCAAGAACCATACGACCAATATCACGAAAATAGTCACGCAAAGCATTGGGATTATCATAAAACGC
+CTCTAATCGGTCGTCAGCCAACGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGCCTGTCGC
+ATTGCATTCATCAAACGCTGAATAGCAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCCAGCAATCTTG
+AACACTCATCCTTAATACCTTTCTTTTTGGGGTAATTATACTCATCGCGAATATCCTTAAGAGGGCGTTC
+AGCAGCCAGCTTGCGGCAAAACTGCGTAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCG
+GGGCGGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCA
+TTAACTTCTCAGTAACAGATACAAACTCATCACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATACAT
+ATCACCATTATCGAACTCAACGCCCTGCATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATGCGGTTA
+TCCATCTGCTTATGGAAGCCAAGCATTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCTCAATAGCAG
+GTTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAGGGTAATAAGAACGAAC
+CATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTAT
+TTCCTAGACAAATTAGAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAA
+CAGCTTTATCAATACCATGAAAAATATCAACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATC
+CTTTGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGATGAACTAAGTCAACC
+TCAGCACTAACCTTGCGAGTCATTTCTTTGATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGAGCTT
+GAGTAAGCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCTTGGAAAGATTGGTGTTTTCCATAATAGA
+CGCAACGCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCATCTCATTTTGTGCATATACCTGGTCTTTC
+GTATTCTGGCGTGAAGTCGCCGACTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATCTCGGCAA
+TCTCTTTCTGATTGTCCAGTTGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCGGCGTCAACCATACC
+AGCAGAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAAGCTCAGGAAATGCAGCAGCAAGATAATCA
+CGAGTATCCTTTCCTTTATCAGCGGCAGACTTGCCACCAAGTCCAACCAAATCAAGCAACTTATCAGAAA
+CGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTTACCAGCTTTAGCCATAGCACCAGAAAC
+AAAACTAGGGACGGCCTCATCAGGGTTAGGAACATTAGAGCCTTGAATGGCAGATTTAATACCAGCATCA
+CCCATGCCTACAGTATTGTTATCGGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGAC
+CGCCTCCAAACAATTTAGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAA
+CATAAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAAACCAATC
+CGCGGCATTTAGTAGCGGTAAAGTTAGACCAAACCATGAAACCAACATAAACATTATTGCCCGGCG

diff -r 000000000000 -r e9c1cdb9f9dc test-data/assembly_test2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assembly_test2.fa Thu Jul 06 17:07:43 2017 -0400

diff -r 000000000000 -r e9c1cdb9f9dc test-data/onp.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/onp.fa Thu Jul 06 17:07:43 2017 -0400

diff -r 000000000000 -r e9c1cdb9f9dc test-data/phix_f.fq.gz

Binary file test-data/phix_f.fq.gz has changed

diff -r 000000000000 -r e9c1cdb9f9dc test-data/phix_r.fq.gz

Binary file test-data/phix_r.fq.gz has changed

diff -r 000000000000 -r e9c1cdb9f9dc unicycler.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/unicycler.xml Thu Jul 06 17:07:43 2017 -0400

[

b'@@ -0,0 +1,483 @@\n+<tool id="unicycler" name="Create assemblies with Unicycler" version="0.2.0">\n+ <requirements>\n+ <requirement type="package" version="0.3.0b">unicycler</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ ## Preparing files\n+\n+ #if str( $paired_unpaired.fastq_input_selector ) == "paired":\n+\n+ #if $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger\'):\n+ ln -s \'${paired_unpaired.fastq_input1}\' fq1.fastq &&\n+ #elif $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger.gz\'):\n+ ln -s \'${paired_unpaired.fastq_input1}\' fq1.fastq.gz &&\n+ #end if\n+\n+ #if $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger\'):\n+ ln -s \'${paired_unpaired.fastq_input2}\' fq2.fastq &&\n+ #elif $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger.gz\'):\n+ ln -s \'${paired_unpaired.fastq_input1}\' fq2.fastq.gz &&\n+ #end if\n+\n+ #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection":\n+\n+ #if $paired_unpaired.fastq_input1.forward.is_of_type(\'fastqsanger\'):\n+ ln -s \'${paired_unpaired.fastq_input1.forward}\' fq1.fastq &&\n+ #elif $paired_unpaired.fastq_input1.forward.is_of_type(\'fastqsanger.gz\'):\n+ ln -s \'${paired_unpaired.fastq_input1.forward}\' fq1.fastq.gz &&\n+ #end if\n+\n+ #if $paired_unpaired.fastq_input1.reverse.is_of_type(\'fastqsanger\'):\n+ ln -s \'${paired_unpaired.fastq_input1.reverse}\' fq2.fastq &&\n+ #elif $paired_unpaired.fastq_input1.reverse.is_of_type(\'fastqsanger.gz\'):\n+ ln -s \'${paired_unpaired.fastq_input2.reverse}\' fq2.fastq.gz &&\n+ #end if\n+\n+ #elif str( $paired_unpaired.fastq_input_selector ) == "single":\n+\n+ #if $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger\'):\n+ ln -s \'${paired_unpaired.fastq_input1}\' fq.fastq &&\n+ #elif $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger.gz\'):\n+ ln -s \'${paired_unpaired.fastq_input1}\' fq.fastq.gz &&\n+ #end if\n+\n+ #end if\n+\n+ ## Get location for pilon installation\n+\n+ pilon=`pilon --jar_dir` &&\n+\n+ #if $long_reads:\n+ #if $long_reads.is_of_type(\'fastqsanger\'):\n+ #set lr = "lr.fastq"\n+ ln -s \'${long_reads}\' lr.fastq &&\n+ #elif $long_reads.is_of_type(\'fastqsanger.gz\'):\n+ #set lr = "lr.fastq.gz"\n+ ln -s \'${long_reads}\' lr.fastq.gz &&\n+ #elif $long_reads.is_of_type(\'fasta\'):\n+ #set lr = "lr.fasta"\n+ ln -s \'${long_reads}\' lr.fasta &&\n+ #end if\n+ #end if\n+\n+ ## Running Unicycler\n+\n+ unicycler -t "\\${GALAXY_SLOTS:-4}"\n+\n+ -o ./\n+ --verbosity 3\n+ --pilon_path \\$pilon\n+\n+ #if str( $paired_unpaired.fastq_input_selector ) != "single":\n+\n+ #if $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger\'):\n+ -1 fq1.fastq\n+ #elif $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger.gz\'):\n+ -1 fq1.fastq.gz\n+ #end if\n+\n+ #if $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger\'):\n+ -2 fq2.fastq\n+ #elif $paired_unpaired.fastq_input2.is_of_type(\'fastqsanger.gz\'):\n+ -2 fq2.fastq.gz\n+ #end if\n+\n+ #else:\n+\n+ #if $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger\'):\n+ -s fq.fastq\n+ #elif $paired_unpaired.fastq_input1.is_of_type(\'fastqsanger.gz\'):\n+ -s fq.fastq.gz\n+ #end if\n+\n+ #end if\n+\n+ #if $long_reads:\n+\n+ -l $lr\n+\n+ #end if\n+\n+ ## General Unicycler Options section\n+ ## ----------------------------------------------------------\n+\n+ --mode \'${uc_opt.mode}\'\n+\n+ #if $uc_opt.min_fasta_length:\n+ --min_fasta_length $uc_opt.min_fasta_length\n+ #end if\n+\n+ #if $uc_opt.lin_seq:\n+ --expected_linear $uc_opt.lin_seq\n+ #end if\n+\n+ $uc_opt.no_correct\n+ $uc_opt.no_rotate\n+\n+ ## Rotation Options section\n+ ## ---------'..b't rotate completed replicons to start at a standard gene**\n+\n+Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence.\n+\n+The following option turns rotation on and off::\n+\n+ --no_rotate\n+ Do not rotate completed replicons\n+ to start at a standard gene\n+ (default: completed replicons are rotated)\n+\n+**Do not use Pilon to polish the final assembly**\n+\n+`Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*.\n+\n+The following option turns pilon part of Unicycler pipeline on and off::\n+\n+ --no_pilon\n+ Do not use Pilon to polish the\n+ final assembly (default: Pilon is used)\n+\n+.. _`Pilon`: https://github.com/broadinstitute/pilon/wiki\n+\n+------\n+\n+**Expected number of linear sequences**\n+\n+If you expect your sample to contain linear (non circular) sequences, set this option::\n+\n+ --expected_linear_seqs EXPECTED_LINEAR_SEQS\n+ The expected number of linear (i.e. non-circular)\n+ sequences in the underlying sequence\n+\n+----\n+\n+**SPAdes options**\n+\n+This section provides control of SPAdes options::\n+\n+ --min_kmer_frac MIN_KMER_FRAC\n+ Lowest k-mer size for SPAdes assembly,\n+ expressed as a fraction of the read length\n+ (default: 0.2)\n+ --max_kmer_frac MAX_KMER_FRAC\n+ Highest k-mer size for SPAdes assembly,\n+ expressed as a fraction of the read length\n+ (default: 0.95)\n+ --kmer_count KMER_COUNT\n+ Number of k-mer steps to use in\n+ SPAdes assembly (default: 10)\n+\n+----\n+\n+**Rotation options**\n+\n+Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation::\n+\n+ --start_genes START_GENES\n+ FASTA file of genes for start point\n+ of rotated replicons\n+ (default: start_genes.fasta)\n+ --start_gene_id START_GENE_ID\n+ The minimum required BLAST percent identity\n+ for a start gene search\n+ (default: 90.0)\n+ --start_gene_cov START_GENE_COV\n+ The minimum required BLAST percent coverage\n+ for a start gene search\n+ (default: 95.0)\n+\n+-----\n+\n+**Graph cleaning options**\n+\n+These options control the removal of small leftover sequences after bridging is complete::\n+\n+ --min_component_size MIN_COMPONENT_SIZE\n+ Unbridged graph components smaller\n+ than this size (bp) will be removed\n+ from the final graph (default: 1000)\n+ --min_dead_end_size MIN_DEAD_END_SIZE\n+ Graph dead ends smaller than this size (bp)\n+ will be removed from the final graph\n+ (default: 1000)\n+\n+-----\n+\n+**Long read alignment options**\n+\n+These options control the alignment of long reads to the assembly graph::\n+\n+ --contamination CONTAMINATION\n+ FASTA file of known contamination in long reads\n+ --scores SCORES\n+ Comma-delimited string of alignment scores:\n+ match, mismatch, gap open, gap extend\n+ (default: 3,-6,-5,-2)\n+ --low_score LOW_SCORE\n+ Score threshold - alignments below this\n+ are considered poor\n+ (default: set threshold automatically)\n+\n+-----\n+\n+**Outputs**\n+\n+Galaxy\'s wrapped for Unicycler produces two outputs:\n+\n+ * final assembly in FASTA format\n+ * final assembly grapth in graph format\n+\n+ While most will likely be interested in the FASTA dataset, the graph dataset is also quite useful and can be visualized using tools such as `Bandage`_.\n+\n+\n+.. _`Bandage`: https://github.com/rrwick/Bandage\n+\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1101/096412</citation>\n+ </citations>\n+</tool>\n'