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annotate seqsero2.xml @ 1:fae43708974d

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planemo upload
author jpayne
date Fri, 09 Nov 2018 11:30:45 -0500
parents 4ff2aee11e5b
children 15572bf93a2a
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jpayne@0 1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0">
jpayne@0 2 <description>Salmonella serotype prediction</description>
jpayne@0 3 <requirements>
jpayne@1 4 <requirement type="package" version="3.6">python</requirement>
jpayne@1 5 <requirement type="package" version="1.70">biopython</requirement>
jpayne@1 6 <requirement type="package" version="2.7.1">blast</requirement>
jpayne@0 7 <requirement type="package" version="1.9">samtools</requirement>
jpayne@1 8 <requirement type="package" version="2.9.1">sra-tools</requirement>
jpayne@0 9 <requirement type="package" version="0.7.17">bwa</requirement>
jpayne@1 10 <requirement type="package" version="3.12.0">spades</requirement>
jpayne@0 11 <requirement type="package" version="2.27.1">bedtools</requirement>
jpayne@0 12 </requirements>
jpayne@0 13 <command detect_errors="exit_code"><![CDATA[
jpayne@0 14 #if $reads.reads_select == 'history'
jpayne@1 15 #set name = $reads.forward.name.split('.')[0].replace(' ','_')
jpayne@0 16 #set forward = $reads.forward
jpayne@0 17 #set reverse = $reads.reverse
jpayne@0 18 #else
jpayne@1 19 #set name = $reads.coll.name.replace(' ', '_')
jpayne@0 20 #set forward = $reads.coll.forward
jpayne@0 21 #set reverse = $reads.coll.reverse
jpayne@0 22 #end if
jpayne@1 23 echo $name ;
jpayne@0 24 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@0 25 gunzip -c $forward > forward.fastq;
jpayne@0 26 #set forward = './forward.fastq'
jpayne@0 27 #end if
jpayne@0 28 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@0 29 gunzip -c $reverse > reverse.fastq;
jpayne@0 30 #set reverse = './reverse.fastq'
jpayne@0 31 #end if
jpayne@0 32 ln -s forward.fastq ${name}_1.fastq;
jpayne@0 33 ln -s reverse.fastq ${name}_2.fastq;
jpayne@1 34 mkdir ./output;
jpayne@1 35 python $__tool_directory__/SeqSero2/SeqSero2_package.py
jpayne@0 36 -p \${GALAXY_SLOTS:-4}
jpayne@1 37 -t 2
jpayne@1 38 -m $mode
jpayne@1 39 -d ./output
jpayne@1 40 -b $maptype
jpayne@1 41 -i ${name}_1.fastq ${name}_2.fastq &&
jpayne@1 42 echo "-=-=-=-=-" &&
jpayne@1 43 cat output/SeqSero_log.txt &&
jpayne@1 44 echo "-=-=-=-=-" &&
jpayne@1 45 ls -lah ./output
jpayne@0 46 ]]></command>
jpayne@0 47 <inputs>
jpayne@0 48
jpayne@1 49 <param label="Analysis mode" type="select" name="mode">
jpayne@1 50 <option value="k">k-mer mode</option>
jpayne@1 51 <option value="a">allele mode</option>
jpayne@1 52 </param>
jpayne@0 53
jpayne@0 54 <conditional name="reads">
jpayne@0 55 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0 56 <option value="collection">Paired collection from your history</option>
jpayne@0 57 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0 58 </param>
jpayne@0 59 <when value="collection">
jpayne@0 60 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
jpayne@0 61 </when>
jpayne@0 62 <when value="history">
jpayne@0 63 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 64 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 65 </when>
jpayne@0 66 </conditional>
jpayne@0 67
jpayne@0 68 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
jpayne@0 69 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
jpayne@0 70 <!-- <param name="numofthr" type="select" label="Number of threads">
jpayne@0 71 <option value="1">1</option>
jpayne@0 72 <option value="2">2</option>
jpayne@0 73 <option value="3">3</option>
jpayne@0 74 <option value="4">4</option> -->
jpayne@0 75 <!-- </param> -->
jpayne@0 76 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
jpayne@0 77 <option value="mem">mem</option>
jpayne@0 78 <option value="sam">sam</option>
jpayne@0 79 </param>
jpayne@0 80
jpayne@0 81
jpayne@0 82 </inputs>
jpayne@0 83 <outputs>
jpayne@1 84 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
jpayne@0 85 </outputs>
jpayne@0 86 <tests>
jpayne@1 87 <!-- <test>
jpayne@1 88 <param name="reads_select" value="history" />
jpayne@1 89 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 90 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 91 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 92 </test>
jpayne@0 93 <test>
jpayne@1 94 <param name="reads_select" value="collection" />
jpayne@1 95 <param name="coll">
jpayne@1 96 <collection type="paired">
jpayne@1 97 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 98 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 99 </collection>
jpayne@1 100 </param>
jpayne@1 101 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 102 </test> -->
jpayne@1 103 <test>
jpayne@1 104 <param name="mode" value="k" />
jpayne@0 105 <param name="reads_select" value="history" />
jpayne@0 106 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 107 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 108 <output name="results" file="Seqsero_result_25k.tsv" />
jpayne@0 109 </test>
jpayne@0 110 <test>
jpayne@1 111 <param name="mode" value="k" />
jpayne@0 112 <param name="reads_select" value="collection" />
jpayne@0 113 <param name="coll">
jpayne@0 114 <collection type="paired">
jpayne@0 115 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 116 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 117 </collection>
jpayne@0 118 </param>
jpayne@1 119 <output name="results" file="Seqsero_result_25k_coll.tsv" />
jpayne@0 120 </test>
jpayne@1 121 <!-- <test>
jpayne@1 122 <param name="mode" value="a" />
jpayne@1 123 <param name="reads_select" value="collection" />
jpayne@1 124 <param name="coll">
jpayne@1 125 <collection type="paired">
jpayne@1 126 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 127 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 128 </collection>
jpayne@1 129 </param>
jpayne@1 130 <output name="results" file="Seqsero_result_allele.tsv" />
jpayne@1 131 </test> -->
jpayne@0 132 </tests>
jpayne@0 133 <help><![CDATA[
jpayne@0 134
jpayne@0 135 **Usage: SeqSero2.py**
jpayne@0 136
jpayne@0 137 **Algorithms for BWA mapping**
jpayne@0 138
jpayne@0 139 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
jpayne@0 140
jpayne@0 141 ]]></help>
jpayne@0 142 <citations>
jpayne@0 143 <citation type="bibtex">
jpayne@0 144 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
jpayne@0 145 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
jpayne@0 146 journal={J Clin Microbiol}, publisher={ASM},
jpayne@0 147 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
jpayne@0 148 year={2015}, month={Max},
jpayne@0 149 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
jpayne@0 150 }</citation>
jpayne@0 151 </citations>
jpayne@0 152
jpayne@0 153 </tool>