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author estrain
date Wed, 02 Oct 2019 16:59:09 -0400
parents 18c8b4d6ab1e
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estrain@1 1 <tool id="seqsero2_v102" name="SeqSero 2 v1.0.2" version="1.0.2">
estrain@0 2 <description>Salmonella serotype prediction</description>
estrain@0 3 <requirements>
estrain@0 4 <requirement type="package" version="3.6">python</requirement>
estrain@0 5 <requirement type="package" version="1.74">biopython</requirement>
estrain@0 6 <requirement type="package" version="2.7.1">blast</requirement>
estrain@0 7 <requirement type="package" version="1.9">samtools</requirement>
estrain@0 8 <requirement type="package" version="2.9.1">sra-tools</requirement>
estrain@0 9 <requirement type="package" version="0.7.17">bwa</requirement>
estrain@0 10 <requirement type="package" version="3.13.1">spades</requirement>
estrain@0 11 <requirement type="package" version="2.27.1">bedtools</requirement>
estrain@0 12 </requirements>
estrain@0 13 <command detect_errors="exit_code"><![CDATA[
estrain@0 14 echo "SeqSero 2 v. 1.0.2" ;
estrain@0 15 mkdir ./output;
estrain@0 16
estrain@0 17 #if $reads.reads_select == 'history'
estrain@0 18 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@0 19 #set $forward = $reads.forward
estrain@0 20 #set $reverse = $reads.reverse
estrain@0 21 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@0 22 #set $tval = 2
estrain@0 23 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@0 24 gunzip -c $reverse > reverse.fastq;
estrain@0 25 #set $reverse = './reverse.fastq'
estrain@0 26 gunzip -c $forward > forward.fastq;
estrain@0 27 #set $forward = './forward.fastq'
estrain@0 28 #end if
estrain@0 29 ln -s $forward ${name}_1.fastq;
estrain@0 30 ln -s $reverse ${name}_2.fastq;
estrain@0 31 #else if $reads.reads_select == 'collection'
estrain@0 32 #set $name = $reads.coll.name.replace(' ', '_')
estrain@0 33 #set $forward = $reads.coll.forward
estrain@0 34 #set $reverse = $reads.coll.reverse
estrain@0 35 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@0 36 #set $tval = 2
estrain@0 37 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@0 38 gunzip -c $reverse > reverse.fastq;
estrain@0 39 #set $reverse = './reverse.fastq'
estrain@0 40 gunzip -c $forward > forward.fastq;
estrain@0 41 #set $forward = './forward.fastq'
estrain@0 42 #end if
estrain@0 43 ln -s $forward ${name}_1.fastq;
estrain@0 44 ln -s $reverse ${name}_2.fastq;
estrain@0 45 #else
estrain@0 46 #set $name = $reads.assembly.name.replace(' ', '_')
estrain@0 47 #set $ga = $reads.assembly
estrain@0 48 #set $infile = $name + ".fasta"
estrain@0 49 ln -s $ga ${name}.fasta;
estrain@0 50 #set $tval = 4
estrain@0 51 #set $mode='k'
estrain@0 52 #end if
estrain@0 53 echo $name ;
estrain@0 54 echo "-=-=-=-=-" ;
estrain@0 55 touch output/SeqSero_log.txt ;
estrain@0 56 python $__tool_directory__/SeqSero2_package.py
estrain@0 57 -p \${GALAXY_SLOTS:-4}
estrain@0 58 -t $tval
estrain@0 59 -m $mode
estrain@0 60 -d ./output
estrain@0 61 #if $mode == 'a':
estrain@0 62 -b $maptype
estrain@0 63 #end if
estrain@0 64 -i $infile &&
estrain@0 65 echo "-=-=-=-=-" &&
estrain@0 66 cat output/SeqSero_log.txt &&
estrain@0 67 echo "-=-=-=-=-" &&
estrain@0 68 ls -lah ./output
estrain@0 69 ]]></command>
estrain@0 70 <inputs>
estrain@0 71
estrain@0 72 <conditional name="reads">
estrain@0 73 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
estrain@0 74 <option value="collection">Paired collection from your history</option>
estrain@0 75 <option value="history">Two FASTQ datasets from your history</option>
estrain@0 76 <option value="genome">Genome Assembly</option>
estrain@0 77 </param>
estrain@0 78 <when value="collection">
estrain@0 79 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
estrain@0 80 </when>
estrain@0 81 <when value="history">
estrain@0 82 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@0 83 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@0 84 </when>
estrain@0 85 <when value="genome">
estrain@0 86 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
estrain@0 87 </when>
estrain@0 88 </conditional>
estrain@0 89
estrain@0 90 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
estrain@0 91 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
estrain@0 92 <!-- <param name="numofthr" type="select" label="Number of threads">
estrain@0 93 <option value="1">1</option>
estrain@0 94 <option value="2">2</option>
estrain@0 95 <option value="3">3</option>
estrain@0 96 <option value="4">4</option> -->
estrain@0 97 <!-- </param> -->
estrain@0 98
estrain@0 99 <param label="Analysis mode" type="select" name="mode">
estrain@0 100 <option value="a">allele mode</option>
estrain@0 101 <option value="k">k-mer mode</option>
estrain@0 102 </param>
estrain@0 103
estrain@0 104 <param name="maptype" type="select" label="Algorithms for BWA mapping">
estrain@0 105 <option value="mem">mem</option>
estrain@0 106 <option value="sam">sam</option>
estrain@0 107 </param>
estrain@0 108
estrain@0 109
estrain@0 110
estrain@0 111 </inputs>
estrain@0 112 <outputs>
estrain@0 113 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/>
estrain@0 114 </outputs>
estrain@0 115 <tests>
estrain@0 116 <!-- <test>
estrain@0 117 <param name="reads_select" value="history" />
estrain@0 118 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 119 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 120 <output name="results" file="Seqsero_result.tsv" />
estrain@0 121 </test>
estrain@0 122 <test>
estrain@0 123 <param name="reads_select" value="collection" />
estrain@0 124 <param name="coll">
estrain@0 125 <collection type="paired">
estrain@0 126 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 127 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 128 </collection>
estrain@0 129 </param>
estrain@0 130 <output name="results" file="Seqsero_result.tsv" />
estrain@0 131 </test> -->
estrain@0 132 <test>
estrain@0 133 <param name="mode" value="k" />
estrain@0 134 <param name="reads_select" value="history" />
estrain@0 135 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
estrain@0 136 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
estrain@0 137 <output name="results" file="Seqsero_result_25k.tsv" />
estrain@0 138 </test>
estrain@0 139 <test>
estrain@0 140 <param name="mode" value="k" />
estrain@0 141 <param name="reads_select" value="collection" />
estrain@0 142 <param name="coll">
estrain@0 143 <collection type="paired">
estrain@0 144 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 145 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 146 </collection>
estrain@0 147 </param>
estrain@0 148 <output name="results" file="Seqsero_result_25k_coll.tsv" />
estrain@0 149 </test>
estrain@0 150 <test>
estrain@0 151 <param name="mode" value="a" />
estrain@0 152 <param name="reads_select" value="history" />
estrain@0 153 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
estrain@0 154 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
estrain@0 155 <assert_stdout>
estrain@0 156 <has_text text="predicted antigenic profile does not exist" />
estrain@0 157 </assert_stdout>
estrain@0 158 </test>
estrain@0 159 <!-- <test>
estrain@0 160 <param name="mode" value="a" />
estrain@0 161 <param name="reads_select" value="collection" />
estrain@0 162 <param name="coll">
estrain@0 163 <collection type="paired">
estrain@0 164 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 165 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@0 166 </collection>
estrain@0 167 </param>
estrain@0 168 <output name="results" file="Seqsero_result_allele.tsv" />
estrain@0 169 </test> -->
estrain@0 170 </tests>
estrain@0 171 <help><![CDATA[
estrain@0 172
estrain@0 173 **Usage: SeqSero2.py**
estrain@0 174
estrain@0 175 **Algorithms for BWA mapping**
estrain@0 176
estrain@0 177 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
estrain@0 178
estrain@0 179 ]]></help>
estrain@0 180 <citations>
estrain@0 181 <citation type="bibtex">
estrain@0 182 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
estrain@0 183 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
estrain@0 184 journal={J Clin Microbiol}, publisher={ASM},
estrain@0 185 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
estrain@0 186 year={2015}, month={Max},
estrain@0 187 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
estrain@0 188 }</citation>
estrain@0 189 <citation type="bibtex">
estrain@0 190 @misc{cfsan_biostatistics_group_2017,
estrain@0 191 title={CFSAN Biostatistics Group fork of SeqSero2},
estrain@0 192 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
estrain@0 193 </citation>
estrain@0 194 </citations>
estrain@0 195
estrain@0 196 </tool>