| Previous changeset 3:c4eac0c7e542 (2018-02-02) Next changeset 5:23300b42ca18 (2018-09-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad |
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modified:
unicycler.xml |
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added:
test-data/only_long.fasta |
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| diff -r c4eac0c7e542 -r 2db911a4efc5 test-data/only_long.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/only_long.fasta Thu Sep 06 10:59:26 2018 -0400 |
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| b'@@ -0,0 +1,80 @@\n+>570cfbe8-1011-441d-911f-d98dcc4472fc_Basecall_1D_template DESKTOP_HT0CTEN_20170425_FNFAE23458_MN19144_sequencing_run_Rap_Bar_nano1_95462_ch100_read2408 /backup2/RawData/nanopore/20170426-nano1/Basecall/workspace/barcode01/0/DESKTOP_HT0CTEN_20170425_FNFAE23458_MN19144_sequencing_run_Rap_Bar_nano1_95462_ch100_read2408.fast5\n+TTGTTGTACTTCGTTCCGGTTACGTATTGCTTCAGAAAGTTGTCCGGTGTCTTTGTGGTTTCATCGTGAAACGCCTTCGCGTTTTTTCGTGCGCCGCTTCACTGGTTTCCTGTGGCTTCGCGGCTGGTTTTACTTGCTTTGTTATAAACCATTTGCCCGCTTCGACATCAGCGGTCAGCGTTTGAACTCATGCGCGAACAGCCCCAACAACTCTTCGCTGCCGGTTACTGCACTTCCAGTTGTTCACAAGGTCAGCTCAAGTTCAACGTCGGTTTTAATCGTCGCCAGCTGGTATGAGATAAACAGCTTCTTTGTTTTTTGCTCGAGCTTCGCTGCCGTGATTTTCGCGCCACGGAAGCTCAACCCGAAAACCGTTTTTCTGGCTCGGCATACAGCGTATCAGTCGAACCTT\n+>b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template DESKTOP_HT0CTEN_20170425_FNFAE23458_MN19144_sequencing_run_Rap_Bar_nano1_95462_ch100_read2617 /backup2/RawData/nanopore/20170426-nano1/Basecall/workspace/barcode01/0/DESKTOP_HT0CTEN_20170425_FNFAE23458_MN19144_sequencing_run_Rap_Bar_nano1_95462_ch100_read2617.fast5\n+TGGTATGCTTCGTTCAGTTACGTATTGCTAGAAAGTTGTCCCATTGTCTTTGTGGTTTTCGCATTTATCGTGAAACGCTTTCGTTTTTCGTGCGCCGCTTCAATTCGTGGTGGCTTTCAGGGCACTCGCGCCGGATTTAGCCGCTAAAATGACGTCCATGCGTTCGTGTGCATAGTATATGCAGACAGAAGAAATCATCAGGCGCGTTTTCACGATATGGACGGGAAAGATGCCGGAAATAGGCAGGAGGACGCAGAAATGCCCTAGGGAGTCTGAGATGGTGCGGGCAACGGATATTATATTAATATACGTTGGTAAGTGTACCAATGCAAGTTTTCAAGTTTTGAGACTCGTTTAGAACATCTAAAAAAAAACACATGAATGCTGCTATAATGAAGCGACTGTTTGATGGTTCATGGTTTACCAGTAGATGAAAACTCAATACAGCGCTATTTAAGAACGCTTAAAATGTACATTCTTGTATTTTTAACGTGCAGAGTAACAGGCTCTAGCTGGTTATGGTACCTCGAAGTTCCTTAGCAAAACAAAGGGACTTTGAAGCTACGCAACCGCCAAGAAGCTCGCTTCAAAGTCCCTGTACCGCAGCTATATTGCATGGGTTTGGTTAAGACATACGTCATGTCTTTGGGGGGCATATTATGGTGAAAAGCTCGCGTCTACACCAATATTTATACATTTCTCTTCAATATTGACGCCGTTCCAGCCAACTTTTGCTATATGGGTGACAATTTTCGCTTTTAAACGGAGATGTCTCCATGATTGAGCATGATCCTAAAATCTGCGTTTTATTGCTGACAGGCATTACCATTCTTTCTATGCTGGAAAACGTGCCGCGTCTTGCATTCTGCTTTTGGCAGTGCGGGAGTCTCAATGAGCTTTAACTACTCCCCTCATAACGCCGTTCGTGTTTTAAGCCGCCTTCTCGATAAGAGTTTCTGAGTGCTGAAGAAATTCGCCTTTACGATAGGTAGAGACGTTGATTGAGAGTGCATCAACAACAGGCTTCTTGTTCCTACGAGCATGAAGATCAGCCGCGATGGTGAGTATGTTCGTGTCTGGTATTTGTCTCAGAAGCCATTGATGACTATTACAACCGTCAGTAGTATCAGTTTAGTCAGCTTGAGGCATGCTGTCATGTTGCTCATCAGCATAGAAGAAGCCTCTACGACCGCTCGTTGCTTTTATCGCTGGGTGAAACTGTCAGAAAGTATCCGTATGATTCTTGTATGATGATTAGGAGGATATTATGTTTCTGGGTTATTTGTTATTTTGCTGGCTTTCTCTACCTATTGAGCTTGGGGTTTCTTCTGGAAACATTGAATGAAGTGCCTCTCATAGATTTGTTTTGGGCTTCATCTGGTCTATAAAACAGTCAGGGAGAGAAGAGTGCTTAAACTTTGATGTTTAGGTCTTAAACTAGACTAAAAAAAGCTCATAATATGCGAGCTTTTATTTATTCATAGACTTGTGTAGTTTTCACTCTTTTTTGCACGGTGTTTCTAAGCCACAAAAAAAAACTTCTGCCTGACCGCCTGTTTGTGGTTGCCTGTTATAAAGTAACAGTAAAAAAATCATGCGTTTCGCAGGAGAAAATATGAGCAAGAGCTATCATAAATCGGCATATTTCCAATAGAGTTCCGTCCTCTTTGAAAGGGGTAGTTCATGAAAAGAGTGGTTCATGGAAGGAAATGTTTATGATTTGGAGTTAGGTGTAAAGGCGCAAAGAAAATATAAGAGATAGTGAAATTCATCATTAAAATGGTGATTGAGAGGCATTATAGAGCACAACTAGGGAAGTTAAAGGAGGAAAAAAGAGCACTCCAATGGTGCCAATGAAGATATTTCTGGTCTGATAGTATAGATCAGATTACATCTAGGCAATCCATGGATATTATAGGTTTCTGTGGATGTTGGTTCCGGTATTAAGTCAATTGTAGATGTAACCGAAGGAAAGAACTGGAAGATTTAGGATACACGAAGTATATGGGATAAGAGTTAGCGATCATTATGCAGAAACTTTTTCTGAGTGAACGGGGATACTCCATTCCAAAGTATAGTCCTTGCAGGATTTTGGTGATTCATATCAAAGATGTAAGTACTACCCACATGCTGTATGAAAGTGCATGAAATAAAGATAGAGAAAAAAAATCTGGAAAATCAAAAGAGTTAAAGAAACGAGCTTTCCTTATGAATCAATAAGCACAAGATCAGTGAGTTGCTTAGAATGATTTTCCATCATAATTTTGTATTAGGTGTTATTAGGAGCGAGACTGAAAGAAAGAAATCTTCGAAGTGGGGGGTTTAACCAAATCTGAAGTTGATATAATCATCAGATCATGACAAAATTTGAGCACCACTTATGGCCAGCAACAGCTATACTTGATGCTGACTTCTTGCATTAAAATAATCAAGTGAAGAGCTCACCTTAAATCTAAGTTAAACGCTTTCTTAAAAGTTCTAATTCCTTGGGCTTAATGGCCGCCAAACACTTGCATGAAGGGTATGTACGCAGCTCATTCTGCCTCTTTACAATCTGCATGTCTTCCAGACAGGTAGGTGCTGCTATTTAGATATAAAGGAAATTTAATTGCTGTTGGGCATGTTCCTAAATTGCAGTGGCCTTTTATAGTGCTGATGATGGAGTGAATGATCATCGCTGTGTCTACAAAGGATGGCAAATGTTACAATGATAAGAAAATTAAGAAAAGATAAAATACAGCAAATGGCCTTTCTGATAAGGTTAAGGGAGTTGTCTGTTCAGTTAACTCAGAACAAGCGAAAAGGTTGCTGAATAATCTACAGGCTGCTCTGTATCATCAATCATTGATACTCTCGCTCTATTCATGCTACTGAAATGGATGCTATTACATCTCTTGTAGACTCGGGAATGGTGG'..b'GCGGAATATCTGCGGGCTTCTCTTTGGCACCGTACGCGCCATAGCTGCATTTTAATACGATGCAGGATAGGGCGGACGCCGCAAAAGTGACGTCACCTGAGCGTTCTGGATACAAAAGGTTAAACAGCGGACAGGAAATGTTTATTGCCACAATATGCTGGCTTATTCACAAAACAGCGGGACAAGATGTGTTTGAGTACCGCCGGCCCATAAGATCTGGTTAGCTCCCACATGTTTGCTATCTTTGCTACCATTTTGCTACTTTTTGCTATCTCCGAGTCTTCTGGTCTTTCAGTTTGCTATCCTTTTGCTACTTTTTTGCTATCAAAATGCTACCTCCTTCTTGCAATAAATGACCAAGGCACGTTAATGATGTATACATCGCCGCGCCGCAAAGTTACGCCTTCCGAATCCGTTCATCACTGTGTGCTGATTAATCCGGGTTAAATCCGACCCCCCTTAGCAATAAAGTACCGCCTGACGGCTGGCCAACGCCCTCACGGTCGCACAGTAAACTGCCGCACCCTTTCACCGTTATGGTGGGGTTCGTAATTGGCTTTCAGGGCGCTCGCCAGTTTTAACCGCTAAAATGACGTCCATGCACGTTCGTGTGCATAGCCATGCAGACGCGAAGGAAATCATCAGGCGCGTTTTTTTTCACATTATGGACGAAGGAAAGATGCCGGAAATAGGCAGGAGGACATAGAAATGCCTGAGGGAGTCTGAGATGGTGCAGGCGGATGTTATGGTAAATAGCTTCCGTTGAGTAAGTATGCCAATGCAAGTTTTTCAGGTTTGAGACTCGTTTAGAACATCTAAAAAAAAAGCACATGAATGCTGCTATAAGAAGCGCGACTGTTTGATGGTTCATGGTTTTACCATTAAGGTAGATGAAAGACTCAATAGCGCTATTTAGAACAGCAATAGCATTCTTGTATTTTTTAACGATGCAGAAATCAGGCTCTAGCTGGAACATGGTACACTCGAAAAGGAGTTCCTTATAGGGACAAAACAAAAGGGACTTTGAGCTACTGCAACCGCCAAGCTCTTCAAAGTCCCTGTACCACAACTATATTACGTGGGTTTGATTTAAGACATACGTCATGTCTTTGAGGGGCATATTATGGTGAAAAACGCGTTCGCGTCTACACCAATATTTATACATTTCTGCTAATATTGACGCGTTTTCCAGCCAACTTTTATATATGGGTGACAATTTTCGCTTTTAAAACGGAGATGTCTCCACCGTTTAAACACCGTCTAAAATCTGCATTTTGTGCTGTACAGGCATTACCATTCTTTCTATGCACAGAAGCGATGCCATCTTGCATTCTGCTTTTTTTTTGGCAATAACGGAGGTGCTCAATGAGCTTTTAACTACTCCCCTCGTTATGCTAACGCCGTTCGTGTTTTAAACCGCCTTCTCGATAAGAGTTTTGCGGAGTGCAGAAGAAATTCGCCCAGCTACGATGATCAAGGGCGGGTGATTAGTGCACATCAACAACAGGCTTCTTGTTCCTGTTTTGAGCATGGGCCAACCGCGATGGTGAGTATGTTCGTGTCTGGTGTTTACATGCAAAGCAAACTGATGACTATTACAACCGTCGTGAGTATCAGTTTAGTCAGCAGGGTATGCTGTCATGTGCTCGTCAGCATAGAAAAAGCATCTACGACGCTCGTTGCTTTTTTATCGCTAGGTGAAACTGTCCCAGAAAGTATCCGTATGATTCTTGCTACTAATGATGATTAGGAGGATATTATGTTTCTGGGGATTTATTTGTTGTTTTGCTGGCTTTCTCTACTATTAGAGAAGCTTGGGTTTCTTCACAGGAAACGCGTTGAATGGGGTACTTACTCTCGCCATATTTGTTTTGGGCTTCATCTGGTCTATGAAGCAGTCGAGTGCTTAAGCACGATGTTTTAGATGTAAACTAAGACTAAAAGCTTTCGCAATATGCGAGCTTTTTTTATTATTTCATAGACTTGTGTAGTTTTCACTCTTTTTTTTGCACGGTGTTCTAAGCAAAAAAAAACTGCGCATTACGCCTGTTTGTGGTTGCCTGTTATAAAGATAACAGTAAAATCCATGCGTTTCGCGGAGAAAATATGAGCAAGAGCTATCGCCTAAATCGTATTTCCCAAAATTTCTACCCCTAAAAGCTATTCACCATGGCTATACTTCTGCTGAAATTGCCACTTTACCAAAACGGCAAGCTACCATCGCCCGCTTAAGCGGCAAAAGCACTGCCATGCCGTACCTTATAGCTGCAGTACCGTAAAACCGCCAGCAGCCAAGAACACGCTGGGCTGGCAAAGCCAGCGCGTACTTAAAAAAGCAGCGCAGGCCGTACGCTTTAGCGAGCCGCCACCGGCAAAACGCAGGCTGCGCGCATTTGCCGTGGCGCACGCGCGCAATTCATGAAATAAAGATAGAAAAAATCTAGAAGGAAAATCAAAGAGAGTTAAAAAACGAACTTTTCATATGAATCAACTAAAACAGATGATTCTTAAGAATAGTTATCAACATAATTTCTATTTGTTAGGTGTTATTGGGAACGAGACTGAAAGAAAAGAAATCTTCGAGATGAGGGTTTAAGCAAATCTGAAGTTGATATAATCATCCATCATGACAGGAGATTTATGAGCACCCATATGGCCAGCAAACAGCAAAAGCTATACTTGATGCTGATATTTTGTTAAAAAATAATCCAAGGCCAGAAACTCACCTTAAATCTAAGAGTTAAACGCTTTCTTGGTCACAATTCATGAGCAATGGCCTTACATAACCTTGCATGAAAGGGCATGTGCGCAGCTCATTCTGTACTCTTTACAATCTGCATGTCTTTCCAGACAGGCTGAGTGCTGCTATTTTAGATATAAAAAGATTTAATTGCTGTTGGGCGCAATGATGTTCCCTAAGTTAACGGTGGCCTTTATAGTGCTGATGATGGAGTGAATGATCATCATCGCTGTGTCTACAAAAGGTGGCAAATGTTACAATAGTAAGAAAATTAAAAATAAAAGATAAAAATACAGCAAATATTGCTTTCTGAAGTAAGGTTAAGGTTGTCTGTTCCAGTTAACTCAAAACAAGCAGAAAAGGTTGTAAGAATAATCTACAGAAGGTACTCCTGTATCATCAATCATTGAGTACTCGCTCTATTCATGCTGAAGTGTGGATGCTATTACATCTCTCTTGCTAGACTCGGGAATGGTGGTTTTTTGAAGAAGATAGGTTTTATATACAACTACGTTCCCCTGTCATAATTGTGCGAGACATATTGTTGCTGTTGGCTCCAATAAAGTTGTTTACATTGAACCTTATGAAAAAGCTTAGCTTTAGAAGTTGCTTTTGATGATGCAATAACTGAAGTTAAGAAAGTGGTAGGTTTTATTTGAGGTCGCTTGTGAAGAAGGGTTTCACCAAGGAGATATCATAAGTTCTTCTTTTCTACAGATGAAAGGAAGGATGAAGTAAAGGTAATGCGGAGAAATATTCAACGAAGTATAAGAATCATATTGATGGCGGTTATTGATAGTTATGGATTTTGAAAATCGTGGATATTTTTCATTAGTAACACAAACAGATGCTGAAGCTCAAGTAGCCGTTCCATCTGGGACGCCAGTTAATCCGCTTCTGCCACCGATTCCTCCGGCATACCAACATCGGTATGAAGATCTGTGACTCTGATGTTACACAGGGGCTTAATCTTGTCTTGCAAAAGAAAAAACCGCTACCAACGGTGGTTTTCAAAATTCTCTGAGCTACCAACTACTTTGAACCGAGGTAACTGGCTTGGAGGAGCTCCGGTCACCAAAACTTGTTCTTTCAGTTTAGCCTTGGCAGGCGCACAACTTCAAGACTAACTCCTCTAAATCAGTTGCAGTGGCTGCTGCCAGTGGCGCTGTCGTGCCTTCTCAGGTTGGACTCAAGACGATAGTTACCGGGGCAGCGCAGCGGTCGGACTGAACGGGGGTTCATTACGCCAGTCAGCTTG\n' 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| diff -r c4eac0c7e542 -r 2db911a4efc5 unicycler.xml --- a/unicycler.xml Fri Feb 02 04:58:08 2018 -0500 +++ b/unicycler.xml Thu Sep 06 10:59:26 2018 -0400 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0"> <macros> - <token name="@VERSION@">0.4.4</token> + <token name="@VERSION@">0.4.6</token> </macros> <requirements> - <requirement type="package" version="@VERSION@">unicycler</requirement> + <requirement type="package" version="@VERSION@">unicycler</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## Preparing files @@ -58,10 +58,13 @@ -o ./ --verbosity 3 --pilon_path \$pilon -#if str( $paired_unpaired.fastq_input_selector ) != "single" +#if str( $paired_unpaired.fastq_input_selector ) == "paired" -1 '$fq1' -2 '$fq2' -#else +#elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" + -1 '$fq1' + -2 '$fq2' +#elif str( $paired_unpaired.fastq_input_selector ) == "single" -s '$fq' #end if #if $long @@ -72,11 +75,17 @@ --mode '$mode' --min_fasta_length '$min_fasta_length' --linear_seqs '$linear_seqs' +#if str($min_anchor_seg_len) != '' +--min_anchor_seg_len '$min_anchor_seg_len' +#end if ## Spades Options section ## ---------------------------------------------------------- $spades.no_correct --min_kmer_frac '$spades.min_kmer_frac' --max_kmer_frac '$spades.max_kmer_frac' +#if str($spades.kmers) != '' +--kmers '$spades.kmers' +#end if --kmer_count '$spades.kmer_count' --depth_filter '$spades.depth_filter' ## Rotation Options section @@ -106,8 +115,6 @@ #if str($lr_align.low_score) != '' --low_score '$lr_align.low_score' #end if -## Miniasm requires racon, which is not available for python 3.x ---no_miniasm ]]></command> <inputs> <conditional name="paired_unpaired"> @@ -115,6 +122,7 @@ <option selected="True" value="paired">Paired</option> <option value="paired_collection">Paired Collection</option> <option value="single">Single</option> + <option value="none">None</option> </param> <when value="paired"> <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> @@ -126,6 +134,8 @@ <when value="single"> <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/> </when> + <when value="none"> + </when> </conditional> <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/> <param argument="--mode" type="select" label="Select Bridging mode"> @@ -135,10 +145,14 @@ </param> <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/> <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/> + <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/> <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!"> <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/> <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> + <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated"> + <validator type="regex" message="Kmers must be comma-separated odd integers (no repitition) without space in the range of 11 to 127 (inclusive)">^(\d*[13579],)*(\d*[13579])$</validator> + </param> <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/> <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/> </section> @@ -312,6 +326,26 @@ </assert_contents> </output> </test> + <test> + <conditional name="paired_unpaired"> + <param name="fastq_input_selector" value="none"/> + </conditional> + <param name="min_anchor_seg_len" value="10"/> + <section name="spades"> + <param name="kmers" value="21,23"/> + </section> + <param name="long" value="only_long.fasta" ftype="fasta" /> + <output name="assembly_graph" ftype="txt"> + <assert_contents> + <has_text text="S" /> + </assert_contents> + </output> + <output name="assembly" ftype="fasta"> + <assert_contents> + <has_text text=">1" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ @@ -434,8 +468,8 @@ Number of k-mer steps to use in SPAdes assembly (default: 10) --depth_filter DEPTH_FILTER - Filter out contigs lower than this fraction - of the chromosomal depth, if doing so does + Filter out contigs lower than this fraction + of the chromosomal depth, if doing so does not result in graph dead ends (default: 0.25) ---- |