Mercurial > repos > jpayne > seqsero_v2

annotate seqsero2.xml @ 0:4ff2aee11e5b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author jpayne
date Tue, 06 Nov 2018 09:45:57 -0500
parents
children fae43708974d
rev   line source
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@0 4 <requirement type="package" version="2.7.10">python</requirement>
jpayne@0 5 <requirement type="package" version="1.60">biopython</requirement>
jpayne@0 6 <requirement type="package" version="2.2.31">blast</requirement>
jpayne@0 7 <requirement type="package" version="1.9">samtools</requirement>
jpayne@0 8 <requirement type="package" version="2.6.2">sra-tools</requirement>
jpayne@0 9 <requirement type="package" version="0.7.17">bwa</requirement>
jpayne@0 10 <requirement type="package" version="3.9.0">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@0 15 #set name = $reads.forward.name.split('_')[0]
jpayne@0 16 #set forward = $reads.forward
jpayne@0 17 #set reverse = $reads.reverse
jpayne@0 18 #else
jpayne@0 19 #set name = $reads.coll.name
jpayne@0 20 #set forward = $reads.coll.forward
jpayne@0 21 #set reverse = $reads.coll.reverse
jpayne@0 22 #end if
jpayne@0 23 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@0 24 gunzip -c $forward > forward.fastq;
jpayne@0 25 #set forward = './forward.fastq'
jpayne@0 26 #end if
jpayne@0 27 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@0 28 gunzip -c $reverse > reverse.fastq;
jpayne@0 29 #set reverse = './reverse.fastq'
jpayne@0 30 #end if
jpayne@0 31 ln -s forward.fastq ${name}_1.fastq;
jpayne@0 32 ln -s reverse.fastq ${name}_2.fastq;
jpayne@0 33 $__tool_directory__/SeqSero2.py
jpayne@0 34 -p \${GALAXY_SLOTS:-4}
jpayne@0 35 -i ${name}_1.fastq ${name}_2.fastq
jpayne@0 36 -b $maptype &&
jpayne@0 37 cat SeqSero_result*/Seqsero_result.tsv > results.tsv
jpayne@0 38
jpayne@0 39 ]]></command>
jpayne@0 40 <inputs>
jpayne@0 41
jpayne@0 42
jpayne@0 43 <conditional name="reads">
jpayne@0 44 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0 45 <option value="collection">Paired collection from your history</option>
jpayne@0 46 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0 47 </param>
jpayne@0 48 <when value="collection">
jpayne@0 49 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
jpayne@0 50 </when>
jpayne@0 51 <when value="history">
jpayne@0 52 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 53 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 54 </when>
jpayne@0 55 </conditional>
jpayne@0 56
jpayne@0 57 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
jpayne@0 58 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
jpayne@0 59 <!-- <param name="numofthr" type="select" label="Number of threads">
jpayne@0 60 <option value="1">1</option>
jpayne@0 61 <option value="2">2</option>
jpayne@0 62 <option value="3">3</option>
jpayne@0 63 <option value="4">4</option> -->
jpayne@0 64 <!-- </param> -->
jpayne@0 65 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
jpayne@0 66 <option value="mem">mem</option>
jpayne@0 67 <option value="sam">sam</option>
jpayne@0 68 </param>
jpayne@0 69
jpayne@0 70
jpayne@0 71 </inputs>
jpayne@0 72 <outputs>
jpayne@0 73 <data format="tsv" label="SeqSero Results" name="results" from_work_dir="results.tsv"/>
jpayne@0 74 </outputs>
jpayne@0 75 <tests>
jpayne@0 76 <test>
jpayne@0 77 <param name="reads_select" value="history" />
jpayne@0 78 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 79 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 80 </test>
jpayne@0 81 <test>
jpayne@0 82 <param name="reads_select" value="collection" />
jpayne@0 83 <param name="coll">
jpayne@0 84 <collection type="paired">
jpayne@0 85 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 86 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 87 </collection>
jpayne@0 88 </param>
jpayne@0 89 </test>
jpayne@0 90 </tests>
jpayne@0 91 <help><![CDATA[
jpayne@0 92
jpayne@0 93 **Usage: SeqSero2.py**
jpayne@0 94
jpayne@0 95 **Algorithms for BWA mapping**
jpayne@0 96
jpayne@0 97 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
jpayne@0 98
jpayne@0 99 ]]></help>
jpayne@0 100 <citations>
jpayne@0 101 <citation type="bibtex">
jpayne@0 102 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
jpayne@0 103 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
jpayne@0 104 journal={J Clin Microbiol}, publisher={ASM},
jpayne@0 105 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
jpayne@0 106 year={2015}, month={Max},
jpayne@0 107 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
jpayne@0 108 }</citation>
jpayne@0 109 </citations>
jpayne@0 110
jpayne@0 111 </tool>