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comparison skesa.xml @ 22:9448df7c25a0 draft

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author estrain
date Mon, 15 Oct 2018 17:12:13 -0400
parents 8bafd3d18864
children e2b708d5c0d3
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21:8bafd3d18864 22:9448df7c25a0
1 <tool id="skesa" name="skesa" version="0.1"> 1 <tool id="skesa" name="skesa" version="0.23">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="2.2">skesa</requirement> 3 <requirement type="package" version="2.3.0">skesa</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6
7 skesa
8 #if $jobtype.select == "asm"
9 --fasta $draft
10 #else if $jobtype.select == "se"
11 --fastq $fastq
12 #else if $jobtype.select == "cl"
13 #set forward=$jobtype.coll.forward
14 #set reverse=$jobtype.coll.reverse
15 --fastq $forward,$reverse --use_paired_ends
16 #else if $jobtype.select == "pe"
17 --fastq $forward,$reverse --use_paired_ends
18 6
7 skesa
8
9 #if $jobtype.select == "fasta_single"
10 #set outname = $jobtype.fasta.name
11 --fasta $jobtype.fasta
12 #else if $jobtype.select == "fastq_single"
13 #set outname = $jobtype.fastq1.name
14 --fastq $jobtype.fastq1
15 #else if $jobtype.select == "fastq_fr"
16 #set outname = $jobtype.fastq1.name
17 --fastq $jobtype.fastq1 --fastq $jobtype.fastq2
18 #else if $jobtype.select == "fastq_pair"
19 #set outname = $jobtype.coll.name
20 --fastq $jobtype.coll.forward --fastq $jobtype.coll.reverse
19 #end if 21 #end if
20 #if $cores != 0 22
21 --cores $cores 23 #if $options.select=="advanced"
24 #if $options.cores
25 --cores $options.cores
26 #end if
27 #if $options.memory
28 --memory $options.memory
29 #end if
30 #if $options.hash_count
31 --hash_count
32 #end if
33 #if $options.estimated_kmers
34 --estimated_kmers $options.estimated.kmers
35 #end if
36 #if $options.skip
37 --skip_bloom_filter
38 #end if
39 #if $options.kmer
40 --kmer $options.kmer
41 #end if
42 #if $options.min_count
43 --min_count $options.min_count
44 #end if
45 #if $options.max_kmer_count
46 --max_kmer_count $options.max_kmer_count
47 #end if
48 #if $options.vector_percent
49 --vector_percent $options.vector_percent
50 #end if
51 #if $options.insert_size
52 --insert_size $options.insert.size
53 #end if
54 #if $options.steps
55 --steps $options.steps
56 #end if
57 #if $options.fraction
58 --fraction $options.fraction
59 #end if
60 #if $options.max_snp_len
61 --max_snp_len $options.max_snp_len
62 #end if
63 #if $options.min_contig
64 --min_contig $options.min_contig
65 #end if
66 #if $options.allow_snps
67 --allow_snps
68 #end if
69 #else if $options.select =="basic"
70 --cores \${GALAXY_SLOTS:-4}
71 --memory 16
22 #end if 72 #end if
23 --memory $memory > results.skesa.fasta 73
24 74 > ${outname}.fasta
25 75
26 ]]></command> 76 ]]></command>
27 <inputs> 77 <inputs>
28 <conditional name="jobtype"> 78 <conditional name="jobtype">
29 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 79 <param name="select" type="select" label="Select Input">
30 <option value="asm">Genome Assembly</option> 80 <option value="fasta_single">Single FASTA</option>
31 <option value="se">Single-End Reads</option> 81 <option value="fastq_single">Single FASTQ</option>
32 <option value="pe">Paired-End Reads (Separate Files)</option> 82 <option value="fastq_fr">Forward and Reverse FASTQ</option>
33 <option value="cl">Paired collection from your history</option> 83 <option value="fastq_pair">Paired FASTQ Collection</option>
34 </param> 84 </param>
35 <when value="asm"> 85 <when value="fasta_single">
36 <param name="draft" type="data" format="fasta" label="FASTA" /> 86 <param name="fasta" type="data" format="fasta" label="FASTA" />
37 </when> 87 </when>
38 <when value="se"> 88 <when value="fastq_single">
39 <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> 89 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
40 </when> 90 </when>
41 <when value="cl"> 91 <when value="fastq_fr">
42 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> 92 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" />
93 <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" />
43 </when> 94 </when>
44 <when value="pe"> 95 <when value="fastq_pair">
45 <param name="forward" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> 96 <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
46 <param name="reverse" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
47 </when> 97 </when>
48 </conditional> 98 </conditional>
49 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" /> 99
50 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" /> 100 <conditional name="options">
51 101 <param name="select" type="select" label="Options Type">
102 <option value="basic">Basic</option>
103 <option value="advanced">Advanced</option>
104 </param>
105 <when value="advanced">
106 <param name="cores" type="integer" label="Number of cores to use" value="1"/>
107 <param name="memory" type="integer" label="Memory available (GB, only for sorted counter)" value="16"/>
108 <param name="hash_count" type="boolean" label="hash counter"/>
109 <param name="estimated_kmers" type="integer" label="Estimated number of unique kmers for bloom filter" value="100"/>
110 <param name="skip" type="boolean" label="skip bloom filter, use estimate kmers as the hash"/>
111 <param name="kmer" type="integer" label="Minimal kmer length for assembly" value="21"/>
112 <param name="min_count" type="integer" label="Minimal count for kmers retained for comparing alternate choices" value=""/>
113 <param name="max_kmer_count" type="integer" label="Minimum acceptable average count for estimating the maximal kmer length in reads" value=""/>
114 <param name="vector_percent" type="float" label="Count for vectors as a fraction of the read number (1=disabled)" value="1">
115 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
116 </param>
117 <param name="insert_size" type="integer" label="Expected insert size for paired reads (if not provided, it will be estimated)" value=""/>
118 <param name="steps" type="integer" label="Number of assembly iterations from minimal to maximal kmer length in reads" value="11"/>
119 <param name="fraction" type="float" label="Maximum noise to signal ratio acceptable for extension" value="0.1">
120 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
121 </param>
122 <param name="max_snp_len" type="integer" label="Maximal snp length" value="150"/>
123 <param name="min_contig" type="integer" label="Minimal contig length reported in output" value="200"/>
124 <param name="allow_snps" type="boolean" label="Turn SNP discovery" value="false"/>
125 </when>
126 <when value="basic"/>
127 </conditional>
52 </inputs> 128 </inputs>
53 <outputs> 129 <outputs>
54 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/> 130 <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/>
55 </outputs> 131 </outputs>
56 132
57 <help><![CDATA[ 133 <help><![CDATA[
58
59 **Usage: skesa**
60
61 **INPUT**
62
63 A fasta assembly or single or paired end reads test or data set list of fastqs
64
65 **Memory available**
66
67 --memory arg (=32) Memory available (GB) [integer]
68
69
70 **Number of cores**
71
72 --cores arg (=0) Number of cores to use (default all) [integer]
73
74 https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/
75 134
76 ]]></help> 135 ]]></help>
77 <citations> 136 <citations>
78 <citation type="bibtex"> 137 <citation type="bibtex">
79 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014, 138 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,