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annotate seqsero2.xml @ 6:5b84740f0463

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planemo upload
author jpayne
date Thu, 18 Apr 2019 16:14:32 -0400
parents e258caab671c
children 87c7eebc6797
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jpayne@6 1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0-65b863a">
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@3 14 #if $reads.reads_select == 'history'
jpayne@3 15 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
jpayne@3 16 #set $forward = $reads.forward
jpayne@3 17 #set $reverse = $reads.reverse
jpayne@0 18 #else
jpayne@3 19 #set $name = $reads.coll.name.replace(' ', '_')
jpayne@3 20 #set $forward = $reads.coll.forward
jpayne@3 21 #set $reverse = $reads.coll.reverse
jpayne@0 22 #end if
jpayne@2 23 echo $name ;
jpayne@2 24 echo "-=-=-=-=-" ;
jpayne@3 25 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@2 26 gunzip -c $forward > forward.fastq;
jpayne@3 27 #set $forward = './forward.fastq'
jpayne@0 28 #end if
jpayne@3 29 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@2 30 gunzip -c $reverse > reverse.fastq;
jpayne@3 31 #set $reverse = './reverse.fastq'
jpayne@0 32 #end if
jpayne@3 33 ln -s $forward ${name}_1.fastq;
jpayne@3 34 ln -s $reverse ${name}_2.fastq;
jpayne@3 35 mkdir ./output;
jpayne@2 36 python $__tool_directory__/SeqSero2/SeqSero2_package.py
jpayne@2 37 -p \${GALAXY_SLOTS:-4}
jpayne@2 38 -t 2
jpayne@2 39 -m $mode
jpayne@2 40 -d ./output
jpayne@2 41 #if $mode == 'a':
jpayne@2 42 -b $maptype
jpayne@2 43 #end if
jpayne@2 44 -i ${name}_1.fastq ${name}_2.fastq &&
jpayne@2 45 echo "-=-=-=-=-" &&
jpayne@2 46 cat output/SeqSero_log.txt &&
jpayne@2 47 echo "-=-=-=-=-" &&
jpayne@2 48 ls -lah ./output
jpayne@0 49 ]]></command>
jpayne@0 50 <inputs>
jpayne@0 51
jpayne@0 52 <conditional name="reads">
jpayne@0 53 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0 54 <option value="collection">Paired collection from your history</option>
jpayne@0 55 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0 56 </param>
jpayne@0 57 <when value="collection">
jpayne@0 58 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
jpayne@0 59 </when>
jpayne@0 60 <when value="history">
jpayne@0 61 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 62 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 63 </when>
jpayne@0 64 </conditional>
jpayne@0 65
jpayne@0 66 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
jpayne@0 67 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
jpayne@0 68 <!-- <param name="numofthr" type="select" label="Number of threads">
jpayne@0 69 <option value="1">1</option>
jpayne@0 70 <option value="2">2</option>
jpayne@0 71 <option value="3">3</option>
jpayne@0 72 <option value="4">4</option> -->
jpayne@0 73 <!-- </param> -->
jpayne@2 74
jpayne@2 75 <param label="Analysis mode" type="select" name="mode">
jpayne@2 76 <option value="k">k-mer mode</option>
jpayne@2 77 <option value="a">allele mode</option>
jpayne@2 78 </param>
jpayne@2 79
jpayne@2 80 <param name="maptype" type="select" label="Algorithms for BWA mapping">
jpayne@0 81 <option value="mem">mem</option>
jpayne@0 82 <option value="sam">sam</option>
jpayne@0 83 </param>
jpayne@2 84
jpayne@0 85
jpayne@0 86
jpayne@0 87 </inputs>
jpayne@0 88 <outputs>
jpayne@1 89 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
jpayne@0 90 </outputs>
jpayne@0 91 <tests>
jpayne@1 92 <!-- <test>
jpayne@1 93 <param name="reads_select" value="history" />
jpayne@1 94 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 95 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 96 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 97 </test>
jpayne@0 98 <test>
jpayne@1 99 <param name="reads_select" value="collection" />
jpayne@1 100 <param name="coll">
jpayne@1 101 <collection type="paired">
jpayne@1 102 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 103 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 104 </collection>
jpayne@1 105 </param>
jpayne@1 106 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 107 </test> -->
jpayne@1 108 <test>
jpayne@1 109 <param name="mode" value="k" />
jpayne@0 110 <param name="reads_select" value="history" />
jpayne@3 111 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
jpayne@3 112 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
jpayne@1 113 <output name="results" file="Seqsero_result_25k.tsv" />
jpayne@0 114 </test>
jpayne@0 115 <test>
jpayne@1 116 <param name="mode" value="k" />
jpayne@0 117 <param name="reads_select" value="collection" />
jpayne@0 118 <param name="coll">
jpayne@0 119 <collection type="paired">
jpayne@0 120 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 121 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 122 </collection>
jpayne@0 123 </param>
jpayne@1 124 <output name="results" file="Seqsero_result_25k_coll.tsv" />
jpayne@0 125 </test>
jpayne@1 126 <!-- <test>
jpayne@1 127 <param name="mode" value="a" />
jpayne@1 128 <param name="reads_select" value="collection" />
jpayne@1 129 <param name="coll">
jpayne@1 130 <collection type="paired">
jpayne@1 131 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 132 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 133 </collection>
jpayne@1 134 </param>
jpayne@1 135 <output name="results" file="Seqsero_result_allele.tsv" />
jpayne@1 136 </test> -->
jpayne@0 137 </tests>
jpayne@0 138 <help><![CDATA[
jpayne@0 139
jpayne@0 140 **Usage: SeqSero2.py**
jpayne@0 141
jpayne@0 142 **Algorithms for BWA mapping**
jpayne@0 143
jpayne@0 144 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
jpayne@0 145
jpayne@0 146 ]]></help>
jpayne@0 147 <citations>
jpayne@0 148 <citation type="bibtex">
jpayne@0 149 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
jpayne@0 150 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
jpayne@0 151 journal={J Clin Microbiol}, publisher={ASM},
jpayne@0 152 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
jpayne@0 153 year={2015}, month={Max},
jpayne@0 154 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
jpayne@0 155 }</citation>
jpayne@5 156 <citation type="bibtex">
jpayne@5 157 @misc{cfsan_biostatistics_group_2017,
jpayne@5 158 title={CFSAN Biostatistics Group fork of SeqSero2},
jpayne@5 159 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
jpayne@5 160 </citation>
jpayne@0 161 </citations>
jpayne@0 162
jpayne@0 163 </tool>