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comparison unicycler.xml @ 4:2db911a4efc5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
author iuc
date Thu, 06 Sep 2018 10:59:26 -0400
parents c4eac0c7e542
children 23300b42ca18
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3:c4eac0c7e542 4:2db911a4efc5
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@">0.4.4</token> 3 <token name="@VERSION@">0.4.6</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[
9 ## Preparing files 9 ## Preparing files
10 #if str( $paired_unpaired.fastq_input_selector ) == "paired" 10 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') 11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
56 ## Running Unicycler 56 ## Running Unicycler
57 unicycler -t "\${GALAXY_SLOTS:-4}" 57 unicycler -t "\${GALAXY_SLOTS:-4}"
58 -o ./ 58 -o ./
59 --verbosity 3 59 --verbosity 3
60 --pilon_path \$pilon 60 --pilon_path \$pilon
61 #if str( $paired_unpaired.fastq_input_selector ) != "single" 61 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
62 -1 '$fq1' 62 -1 '$fq1'
63 -2 '$fq2' 63 -2 '$fq2'
64 #else 64 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
65 -1 '$fq1'
66 -2 '$fq2'
67 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
65 -s '$fq' 68 -s '$fq'
66 #end if 69 #end if
67 #if $long 70 #if $long
68 -l $lr 71 -l $lr
69 #end if 72 #end if
70 ## General Unicycler Options section 73 ## General Unicycler Options section
71 ## ---------------------------------------------------------- 74 ## ----------------------------------------------------------
72 --mode '$mode' 75 --mode '$mode'
73 --min_fasta_length '$min_fasta_length' 76 --min_fasta_length '$min_fasta_length'
74 --linear_seqs '$linear_seqs' 77 --linear_seqs '$linear_seqs'
78 #if str($min_anchor_seg_len) != ''
79 --min_anchor_seg_len '$min_anchor_seg_len'
80 #end if
75 ## Spades Options section 81 ## Spades Options section
76 ## ---------------------------------------------------------- 82 ## ----------------------------------------------------------
77 $spades.no_correct 83 $spades.no_correct
78 --min_kmer_frac '$spades.min_kmer_frac' 84 --min_kmer_frac '$spades.min_kmer_frac'
79 --max_kmer_frac '$spades.max_kmer_frac' 85 --max_kmer_frac '$spades.max_kmer_frac'
86 #if str($spades.kmers) != ''
87 --kmers '$spades.kmers'
88 #end if
80 --kmer_count '$spades.kmer_count' 89 --kmer_count '$spades.kmer_count'
81 --depth_filter '$spades.depth_filter' 90 --depth_filter '$spades.depth_filter'
82 ## Rotation Options section 91 ## Rotation Options section
83 ## ---------------------------------------------------------- 92 ## ----------------------------------------------------------
84 $rotation.no_rotate 93 $rotation.no_rotate
104 #end if 113 #end if
105 --scores '${lr_align.scores}' 114 --scores '${lr_align.scores}'
106 #if str($lr_align.low_score) != '' 115 #if str($lr_align.low_score) != ''
107 --low_score '$lr_align.low_score' 116 --low_score '$lr_align.low_score'
108 #end if 117 #end if
109 ## Miniasm requires racon, which is not available for python 3.x
110 --no_miniasm
111 ]]></command> 118 ]]></command>
112 <inputs> 119 <inputs>
113 <conditional name="paired_unpaired"> 120 <conditional name="paired_unpaired">
114 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data"> 121 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
115 <option selected="True" value="paired">Paired</option> 122 <option selected="True" value="paired">Paired</option>
116 <option value="paired_collection">Paired Collection</option> 123 <option value="paired_collection">Paired Collection</option>
117 <option value="single">Single</option> 124 <option value="single">Single</option>
125 <option value="none">None</option>
118 </param> 126 </param>
119 <when value="paired"> 127 <when value="paired">
120 <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" label="Select first set of reads" help="Specify dataset with forward reads"/>
121 <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 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
122 </when> 130 </when>
124 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> 132 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
125 </when> 133 </when>
126 <when value="single"> 134 <when value="single">
127 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/> 135 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
128 </when> 136 </when>
137 <when value="none">
138 </when>
129 </conditional> 139 </conditional>
130 <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"/> 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"/>
131 <param argument="--mode" type="select" label="Select Bridging mode"> 141 <param argument="--mode" type="select" label="Select Bridging mode">
132 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> 142 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
133 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> 143 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
134 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> 144 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
135 </param> 145 </param>
136 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/> 146 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>
137 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/> 147 <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"/>
138 <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!"> 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!">
139 <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."/> 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."/>
140 <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"/> 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"/>
141 <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"/> 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"/>
153 <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>
155 </param>
142 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/> 156 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
143 <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"/> 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"/>
144 </section> 158 </section>
145 <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!"> 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!">
146 <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."/> 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."/>
310 <assert_contents> 324 <assert_contents>
311 <has_text text="length=5386" /> 325 <has_text text="length=5386" />
312 </assert_contents> 326 </assert_contents>
313 </output> 327 </output>
314 </test> 328 </test>
329 <test>
330 <conditional name="paired_unpaired">
331 <param name="fastq_input_selector" value="none"/>
332 </conditional>
333 <param name="min_anchor_seg_len" value="10"/>
334 <section name="spades">
335 <param name="kmers" value="21,23"/>
336 </section>
337 <param name="long" value="only_long.fasta" ftype="fasta" />
338 <output name="assembly_graph" ftype="txt">
339 <assert_contents>
340 <has_text text="S" />
341 </assert_contents>
342 </output>
343 <output name="assembly" ftype="fasta">
344 <assert_contents>
345 <has_text text=">1" />
346 </assert_contents>
347 </output>
348 </test>
315 </tests> 349 </tests>
316 <help><![CDATA[ 350 <help><![CDATA[
317 351
318 **Unicycler** 352 **Unicycler**
319 353
432 (default: 0.95) 466 (default: 0.95)
433 --kmer_count KMER_COUNT 467 --kmer_count KMER_COUNT
434 Number of k-mer steps to use in 468 Number of k-mer steps to use in
435 SPAdes assembly (default: 10) 469 SPAdes assembly (default: 10)
436 --depth_filter DEPTH_FILTER 470 --depth_filter DEPTH_FILTER
437 Filter out contigs lower than this fraction 471 Filter out contigs lower than this fraction
438 of the chromosomal depth, if doing so does 472 of the chromosomal depth, if doing so does
439 not result in graph dead ends (default: 0.25) 473 not result in graph dead ends (default: 0.25)
440 474
441 ---- 475 ----
442 476
443 **Rotation options** 477 **Rotation options**