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author estrain
date Sat, 07 Sep 2019 20:38:09 -0400
parents 526617c6f359
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estrain@39 1 <tool id="seqsero2_v1_0_1" name="SeqSero 2 v1.0.1" version="1.0.1">
estrain@8 2 <description>Salmonella serotype prediction</description>
estrain@8 3 <requirements>
estrain@38 4 <requirement type="package" version="3.6">python</requirement>
estrain@38 5 <requirement type="package" version="1.74">biopython</requirement>
estrain@38 6 <requirement type="package" version="2.7.1">blast</requirement>
estrain@38 7 <requirement type="package" version="1.9">samtools</requirement>
estrain@38 8 <requirement type="package" version="2.9.1">sra-tools</requirement>
estrain@38 9 <requirement type="package" version="0.7.17">bwa</requirement>
estrain@38 10 <requirement type="package" version="3.13.1">spades</requirement>
estrain@38 11 <requirement type="package" version="2.27.1">bedtools</requirement>
estrain@8 12 </requirements>
estrain@8 13 <command detect_errors="exit_code"><![CDATA[
estrain@8 14 echo "SeqSero 2 v. 1.0.1" ;
estrain@27 15 mkdir ./output;
estrain@20 16
estrain@8 17 #if $reads.reads_select == 'history'
estrain@27 18 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@27 19 #set $forward = $reads.forward
estrain@27 20 #set $reverse = $reads.reverse
estrain@41 21 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@41 22 #set $tval = 2
estrain@41 23 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@41 24 gunzip -c $reverse > reverse.fastq;
estrain@41 25 #set $reverse = './reverse.fastq'
estrain@41 26 gunzip -c $forward > forward.fastq;
estrain@41 27 #set $forward = './forward.fastq'
estrain@41 28 #end if
estrain@41 29 ln -s $forward ${name}_1.fastq;
estrain@41 30 ln -s $reverse ${name}_2.fastq;
estrain@41 31 #else if $reads.reads_select == 'collection'
estrain@27 32 #set $name = $reads.coll.name.replace(' ', '_')
estrain@27 33 #set $forward = $reads.coll.forward
estrain@27 34 #set $reverse = $reads.coll.reverse
estrain@41 35 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@41 36 #set $tval = 2
estrain@41 37 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@41 38 gunzip -c $reverse > reverse.fastq;
estrain@41 39 #set $reverse = './reverse.fastq'
estrain@41 40 gunzip -c $forward > forward.fastq;
estrain@41 41 #set $forward = './forward.fastq'
estrain@41 42 #end if
estrain@41 43 ln -s $forward ${name}_1.fastq;
estrain@41 44 ln -s $reverse ${name}_2.fastq;
estrain@41 45 #else
estrain@41 46 #set $name = $reads.assembly.name.replace(' ', '_')
estrain@41 47 #set $ga = $reads.assembly
estrain@41 48 #set $infile = $name + ".fasta"
estrain@41 49 ln -s $ga ${name}.fasta;
estrain@41 50 #set $tval = 4
estrain@41 51 #set $mode='k'
estrain@8 52 #end if
estrain@27 53 echo $name ;
estrain@27 54 echo "-=-=-=-=-" ;
estrain@27 55 touch output/SeqSero_log.txt ;
estrain@38 56 python $__tool_directory__/SeqSero2_package.py
estrain@8 57 -p \${GALAXY_SLOTS:-4}
estrain@41 58 -t $tval
estrain@8 59 -m $mode
estrain@8 60 -d ./output
estrain@8 61 #if $mode == 'a':
estrain@8 62 -b $maptype
estrain@8 63 #end if
estrain@41 64 -i $infile &&
estrain@8 65 echo "-=-=-=-=-" &&
estrain@8 66 cat output/SeqSero_log.txt &&
estrain@8 67 echo "-=-=-=-=-" &&
estrain@8 68 ls -lah ./output
estrain@8 69 ]]></command>
estrain@8 70 <inputs>
estrain@8 71
estrain@8 72 <conditional name="reads">
estrain@41 73 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
estrain@8 74 <option value="collection">Paired collection from your history</option>
estrain@8 75 <option value="history">Two FASTQ datasets from your history</option>
estrain@41 76 <option value="genome">Genome Assembly</option>
estrain@8 77 </param>
estrain@8 78 <when value="collection">
estrain@8 79 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
estrain@8 80 </when>
estrain@8 81 <when value="history">
estrain@8 82 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@8 83 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@8 84 </when>
estrain@41 85 <when value="genome">
estrain@41 86 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
estrain@41 87 </when>
estrain@8 88 </conditional>
estrain@8 89
estrain@8 90 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
estrain@8 91 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
estrain@8 92 <!-- <param name="numofthr" type="select" label="Number of threads">
estrain@8 93 <option value="1">1</option>
estrain@8 94 <option value="2">2</option>
estrain@8 95 <option value="3">3</option>
estrain@8 96 <option value="4">4</option> -->
estrain@8 97 <!-- </param> -->
estrain@8 98
estrain@8 99 <param label="Analysis mode" type="select" name="mode">
estrain@8 100 <option value="a">allele mode</option>
estrain@41 101 <option value="k">k-mer mode</option>
estrain@8 102 </param>
estrain@8 103
estrain@8 104 <param name="maptype" type="select" label="Algorithms for BWA mapping">
estrain@8 105 <option value="mem">mem</option>
estrain@8 106 <option value="sam">sam</option>
estrain@8 107 </param>
estrain@8 108
estrain@8 109
estrain@8 110
estrain@8 111 </inputs>
estrain@8 112 <outputs>
estrain@12 113 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/>
estrain@8 114 </outputs>
estrain@8 115 <tests>
estrain@8 116 <!-- <test>
estrain@8 117 <param name="reads_select" value="history" />
estrain@8 118 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 119 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 120 <output name="results" file="Seqsero_result.tsv" />
estrain@8 121 </test>
estrain@8 122 <test>
estrain@8 123 <param name="reads_select" value="collection" />
estrain@8 124 <param name="coll">
estrain@8 125 <collection type="paired">
estrain@8 126 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 127 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 128 </collection>
estrain@8 129 </param>
estrain@8 130 <output name="results" file="Seqsero_result.tsv" />
estrain@8 131 </test> -->
estrain@8 132 <test>
estrain@8 133 <param name="mode" value="k" />
estrain@8 134 <param name="reads_select" value="history" />
estrain@8 135 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
estrain@8 136 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
estrain@8 137 <output name="results" file="Seqsero_result_25k.tsv" />
estrain@8 138 </test>
estrain@8 139 <test>
estrain@8 140 <param name="mode" value="k" />
estrain@8 141 <param name="reads_select" value="collection" />
estrain@8 142 <param name="coll">
estrain@8 143 <collection type="paired">
estrain@8 144 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 145 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 146 </collection>
estrain@8 147 </param>
estrain@8 148 <output name="results" file="Seqsero_result_25k_coll.tsv" />
estrain@8 149 </test>
estrain@8 150 <test>
estrain@8 151 <param name="mode" value="a" />
estrain@8 152 <param name="reads_select" value="history" />
estrain@8 153 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
estrain@8 154 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
estrain@8 155 <assert_stdout>
estrain@8 156 <has_text text="predicted antigenic profile does not exist" />
estrain@8 157 </assert_stdout>
estrain@8 158 </test>
estrain@8 159 <!-- <test>
estrain@8 160 <param name="mode" value="a" />
estrain@8 161 <param name="reads_select" value="collection" />
estrain@8 162 <param name="coll">
estrain@8 163 <collection type="paired">
estrain@8 164 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 165 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 166 </collection>
estrain@8 167 </param>
estrain@8 168 <output name="results" file="Seqsero_result_allele.tsv" />
estrain@8 169 </test> -->
estrain@8 170 </tests>
estrain@8 171 <help><![CDATA[
estrain@8 172
estrain@8 173 **Usage: SeqSero2.py**
estrain@8 174
estrain@8 175 **Algorithms for BWA mapping**
estrain@8 176
estrain@8 177 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
estrain@8 178
estrain@8 179 ]]></help>
estrain@8 180 <citations>
estrain@8 181 <citation type="bibtex">
estrain@8 182 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
estrain@8 183 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
estrain@8 184 journal={J Clin Microbiol}, publisher={ASM},
estrain@8 185 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
estrain@8 186 year={2015}, month={Max},
estrain@8 187 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
estrain@8 188 }</citation>
estrain@8 189 <citation type="bibtex">
estrain@8 190 @misc{cfsan_biostatistics_group_2017,
estrain@8 191 title={CFSAN Biostatistics Group fork of SeqSero2},
estrain@8 192 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
estrain@8 193 </citation>
estrain@8 194 </citations>
estrain@8 195
estrain@8 196 </tool>