| Previous changeset 5:23300b42ca18 (2018-09-19) Next changeset 7:88c240872a65 (2019-10-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5 |
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modified:
unicycler.xml |
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| diff -r 23300b42ca18 -r 0a3a602cd1e3 unicycler.xml --- a/unicycler.xml Wed Sep 19 17:07:02 2018 -0400 +++ b/unicycler.xml Sat Feb 09 17:02:48 2019 -0500 |
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| b'@@ -1,6 +1,6 @@\n <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0">\n <macros>\n- <token name="@VERSION@">0.4.6</token>\n+ <token name="@VERSION@">0.4.7</token>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">unicycler</requirement>\n@@ -125,14 +125,17 @@\n <option value="none">None</option>\n </param>\n <when value="paired">\n- <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>\n- <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>\n+ <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz"\n+ label="Select first set of reads" help="Specify dataset with forward reads"/>\n+ <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz"\n+ label="Select second set of reads" help="Specify dataset with reverse reads"/>\n </when>\n <when value="paired_collection">\n <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />\n </when>\n <when value="single">\n- <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/>\n+ <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz"\n+ label="Select unpaired reads" help="Specify dataset with unpaired reads"/>\n </when>\n <when value="none">\n </when>\n@@ -146,34 +149,47 @@\n <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>\n <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>\n <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>\n- <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!">\n- <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."/>\n- <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"/>\n- <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"/>\n+ <section name="spades" expanded="False" title="SPAdes options"\n+ 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!">\n+ <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue=""\n+ label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>\n+ <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2"\n+ label="Lowest k-mer size for S'..b' label="Do not rotate completed replicons to start at a standard gene." help="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 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" />\n <param argument="--start_gene_id" type="float" min="0" max="100" value="90" label="The minimum required BLAST percent identity for a start gene search"/>\n <param argument="--start_gene_cov" type="float" min="0" max="100" value="95" label="The minimum required BLAST percent coverage for a start gene search"/>\n </section>\n <section name="pilon" title="Pilon options" expanded="false">\n- <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue="" label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>\n+ <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue=""\n+ label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>\n <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/>\n </section>\n- <section name="graph_clean" expanded="false" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete.">\n- <param argument="--min_component_size" type="integer" min="0" value="1000" label="Unbridged graph components smaller than this size will be removed from the final graph" />\n- <param argument="--min_dead_end_size" type="integer" min="0" value="1000" label="Graph dead ends smaller than this size will be removed from the final graph"/>\n+ <section name="graph_clean" expanded="false" title="Graph cleaning options"\n+ help="These options control the removal of small leftover sequences after bridging is complete.">\n+ <param argument="--min_component_size" type="integer" min="0" value="1000"\n+ label="Unbridged graph components smaller than this size will be removed from the final graph" />\n+ <param argument="--min_dead_end_size" type="integer" min="0" value="1000"\n+ label="Graph dead ends smaller than this size will be removed from the final graph"/>\n </section>\n <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">\n- <param argument="--contamination" optional="true" type="data" format="fasta" label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />\n+ <param argument="--contamination" optional="true" type="data" format="fasta"\n+ label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />\n <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>\n- <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>\n+ <param argument="--low_score" optional="true" type="integer" value=""\n+ label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>\n </section>\n </inputs>\n <outputs>\n' |