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annotate seqsero2.xml @ 13:3513b93ebe6a

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planemo upload
author jpayne
date Tue, 03 Sep 2019 12:40:46 -0400
parents 4ac593d4b40f
children 496f5f2b5e75
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jpayne@10 1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0.1">
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@12 10 <requirement type="package" version="3.13.1">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@10 14 echo "SeqSero 2 v. 1.0.0" ;
jpayne@3 15 #if $reads.reads_select == 'history'
jpayne@3 16 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
jpayne@3 17 #set $forward = $reads.forward
jpayne@3 18 #set $reverse = $reads.reverse
jpayne@0 19 #else
jpayne@3 20 #set $name = $reads.coll.name.replace(' ', '_')
jpayne@3 21 #set $forward = $reads.coll.forward
jpayne@3 22 #set $reverse = $reads.coll.reverse
jpayne@0 23 #end if
jpayne@2 24 echo $name ;
jpayne@2 25 echo "-=-=-=-=-" ;
jpayne@3 26 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@2 27 gunzip -c $forward > forward.fastq;
jpayne@3 28 #set $forward = './forward.fastq'
jpayne@0 29 #end if
jpayne@3 30 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@2 31 gunzip -c $reverse > reverse.fastq;
jpayne@3 32 #set $reverse = './reverse.fastq'
jpayne@0 33 #end if
jpayne@3 34 ln -s $forward ${name}_1.fastq;
jpayne@3 35 ln -s $reverse ${name}_2.fastq;
jpayne@3 36 mkdir ./output;
jpayne@12 37 touch output/SeqSero_log.txt ;
jpayne@2 38 python $__tool_directory__/SeqSero2/SeqSero2_package.py
jpayne@2 39 -p \${GALAXY_SLOTS:-4}
jpayne@2 40 -t 2
jpayne@2 41 -m $mode
jpayne@2 42 -d ./output
jpayne@2 43 #if $mode == 'a':
jpayne@2 44 -b $maptype
jpayne@2 45 #end if
jpayne@2 46 -i ${name}_1.fastq ${name}_2.fastq &&
jpayne@2 47 echo "-=-=-=-=-" &&
jpayne@2 48 cat output/SeqSero_log.txt &&
jpayne@2 49 echo "-=-=-=-=-" &&
jpayne@2 50 ls -lah ./output
jpayne@0 51 ]]></command>
jpayne@0 52 <inputs>
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@2 76
jpayne@2 77 <param label="Analysis mode" type="select" name="mode">
jpayne@13 78 <option value="a">allele mode</option>
jpayne@2 79 <option value="k">k-mer mode</option>
jpayne@2 80 </param>
jpayne@2 81
jpayne@2 82 <param name="maptype" type="select" label="Algorithms for BWA mapping">
jpayne@0 83 <option value="mem">mem</option>
jpayne@0 84 <option value="sam">sam</option>
jpayne@0 85 </param>
jpayne@2 86
jpayne@0 87
jpayne@0 88
jpayne@0 89 </inputs>
jpayne@0 90 <outputs>
jpayne@1 91 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
jpayne@0 92 </outputs>
jpayne@0 93 <tests>
jpayne@1 94 <!-- <test>
jpayne@1 95 <param name="reads_select" value="history" />
jpayne@1 96 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 97 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 98 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 99 </test>
jpayne@0 100 <test>
jpayne@1 101 <param name="reads_select" value="collection" />
jpayne@1 102 <param name="coll">
jpayne@1 103 <collection type="paired">
jpayne@1 104 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 105 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 106 </collection>
jpayne@1 107 </param>
jpayne@1 108 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 109 </test> -->
jpayne@1 110 <test>
jpayne@1 111 <param name="mode" value="k" />
jpayne@0 112 <param name="reads_select" value="history" />
jpayne@3 113 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
jpayne@3 114 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
jpayne@1 115 <output name="results" file="Seqsero_result_25k.tsv" />
jpayne@0 116 </test>
jpayne@0 117 <test>
jpayne@1 118 <param name="mode" value="k" />
jpayne@0 119 <param name="reads_select" value="collection" />
jpayne@0 120 <param name="coll">
jpayne@0 121 <collection type="paired">
jpayne@0 122 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 123 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 124 </collection>
jpayne@0 125 </param>
jpayne@1 126 <output name="results" file="Seqsero_result_25k_coll.tsv" />
jpayne@0 127 </test>
jpayne@11 128 <test>
jpayne@11 129 <param name="mode" value="a" />
jpayne@11 130 <param name="reads_select" value="history" />
jpayne@12 131 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
jpayne@12 132 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
jpayne@12 133 <assert_stdout>
jpayne@12 134 <has_text text="predicted antigenic profile does not exist" />
jpayne@12 135 </assert_stdout>
jpayne@11 136 </test>
jpayne@1 137 <!-- <test>
jpayne@1 138 <param name="mode" value="a" />
jpayne@1 139 <param name="reads_select" value="collection" />
jpayne@1 140 <param name="coll">
jpayne@1 141 <collection type="paired">
jpayne@1 142 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 143 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 144 </collection>
jpayne@1 145 </param>
jpayne@1 146 <output name="results" file="Seqsero_result_allele.tsv" />
jpayne@1 147 </test> -->
jpayne@0 148 </tests>
jpayne@0 149 <help><![CDATA[
jpayne@0 150
jpayne@0 151 **Usage: SeqSero2.py**
jpayne@0 152
jpayne@0 153 **Algorithms for BWA mapping**
jpayne@0 154
jpayne@0 155 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
jpayne@0 156
jpayne@0 157 ]]></help>
jpayne@0 158 <citations>
jpayne@0 159 <citation type="bibtex">
jpayne@0 160 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
jpayne@0 161 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
jpayne@0 162 journal={J Clin Microbiol}, publisher={ASM},
jpayne@0 163 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
jpayne@0 164 year={2015}, month={Max},
jpayne@0 165 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
jpayne@0 166 }</citation>
jpayne@5 167 <citation type="bibtex">
jpayne@5 168 @misc{cfsan_biostatistics_group_2017,
jpayne@5 169 title={CFSAN Biostatistics Group fork of SeqSero2},
jpayne@5 170 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
jpayne@5 171 </citation>
jpayne@0 172 </citations>
jpayne@0 173
jpayne@0 174 </tool>