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comparison unicycler.xml @ 6:0a3a602cd1e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
author iuc
date Sat, 09 Feb 2019 17:02:48 -0500
parents 23300b42ca18
children 88c240872a65
comparison
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5:23300b42ca18 6:0a3a602cd1e3
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0"> 1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0">
2 <macros> 2 <macros>
3 <token name="@VERSION@">0.4.6</token> 3 <token name="@VERSION@">0.4.7</token>
4 </macros> 4 </macros>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@VERSION@">unicycler</requirement> 6 <requirement type="package" version="@VERSION@">unicycler</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
123 <option value="paired_collection">Paired Collection</option> 123 <option value="paired_collection">Paired Collection</option>
124 <option value="single">Single</option> 124 <option value="single">Single</option>
125 <option value="none">None</option> 125 <option value="none">None</option>
126 </param> 126 </param>
127 <when value="paired"> 127 <when value="paired">
128 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> 128 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz"
129 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> 129 label="Select first set of reads" help="Specify dataset with forward reads"/>
130 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz"
131 label="Select second set of reads" help="Specify dataset with reverse reads"/>
130 </when> 132 </when>
131 <when value="paired_collection"> 133 <when value="paired_collection">
132 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> 134 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
133 </when> 135 </when>
134 <when value="single"> 136 <when value="single">
135 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/> 137 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz"
138 label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
136 </when> 139 </when>
137 <when value="none"> 140 <when value="none">
138 </when> 141 </when>
139 </conditional> 142 </conditional>
140 <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"/> 143 <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"/>
144 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> 147 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
145 </param> 148 </param>
146 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/> 149 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>
147 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/> 150 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
148 <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/> 151 <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>
149 <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!"> 152 <section name="spades" expanded="False" title="SPAdes options"
150 <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."/> 153 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!">
151 <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"/> 154 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue=""
152 <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"/> 155 label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
156 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2"
157 label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
158 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95"
159 label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
153 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated"> 160 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated">
154 <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])$</validator> 161 <validator type="regex" message="Kmers must be comma-separated odd integers (no repitition) without space in the range of 11 to 127 (inclusive)">^(\d*[13579],)*(\d*[13579])$</validator>
155 </param> 162 </param>
156 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/> 163 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
157 <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"/> 164 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25"
165 label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
158 </section> 166 </section>
159 <section name="rotation" expanded="false" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!"> 167 <section name="rotation" expanded="false" title="Rotation options"
160 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" 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."/> 168 help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
169 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue=""
170 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."/>
161 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" /> 171 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" />
162 <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"/> 172 <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"/>
163 <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"/> 173 <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"/>
164 </section> 174 </section>
165 <section name="pilon" title="Pilon options" expanded="false"> 175 <section name="pilon" title="Pilon options" expanded="false">
166 <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."/> 176 <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue=""
177 label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>
167 <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/> 178 <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/>
168 </section> 179 </section>
169 <section name="graph_clean" expanded="false" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete."> 180 <section name="graph_clean" expanded="false" title="Graph cleaning options"
170 <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" /> 181 help="These options control the removal of small leftover sequences after bridging is complete.">
171 <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"/> 182 <param argument="--min_component_size" type="integer" min="0" value="1000"
183 label="Unbridged graph components smaller than this size will be removed from the final graph" />
184 <param argument="--min_dead_end_size" type="integer" min="0" value="1000"
185 label="Graph dead ends smaller than this size will be removed from the final graph"/>
172 </section> 186 </section>
173 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph."> 187 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
174 <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." /> 188 <param argument="--contamination" optional="true" type="data" format="fasta"
189 label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
175 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/> 190 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
176 <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> 191 <param argument="--low_score" optional="true" type="integer" value=""
192 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
177 </section> 193 </section>
178 </inputs> 194 </inputs>
179 <outputs> 195 <outputs>
180 <data name="assembly_graph" format="tabular" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> 196 <data name="assembly_graph" format="tabular" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
181 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> 197 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>