Mercurial > repos > estrain > seqsero2_v1_0_2

annotate seqsero2.xml @ 1:0d922d9b5233 tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Wed, 02 Oct 2019 16:11:20 -0400
parents
children
rev   line source
estrain@1 1 <tool id="seqsero2_v1_0_2" name="SeqSero 2 v1.0.2" version="1.0.2">
estrain@1 2 <description>Salmonella serotype prediction</description>
estrain@1 3 <requirements>
estrain@1 4 <requirement type="package" version="3.6">python</requirement>
estrain@1 5 <requirement type="package" version="1.74">biopython</requirement>
estrain@1 6 <requirement type="package" version="2.7.1">blast</requirement>
estrain@1 7 <requirement type="package" version="1.9">samtools</requirement>
estrain@1 8 <requirement type="package" version="2.9.1">sra-tools</requirement>
estrain@1 9 <requirement type="package" version="0.7.17">bwa</requirement>
estrain@1 10 <requirement type="package" version="3.13.1">spades</requirement>
estrain@1 11 <requirement type="package" version="2.27.1">bedtools</requirement>
estrain@1 12 </requirements>
estrain@1 13 <command detect_errors="exit_code"><![CDATA[
estrain@1 14 echo "SeqSero 2 v. 1.0.2" ;
estrain@1 15 mkdir ./output;
estrain@1 16
estrain@1 17 #if $reads.reads_select == 'history'
estrain@1 18 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@1 19 #set $forward = $reads.forward
estrain@1 20 #set $reverse = $reads.reverse
estrain@1 21 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@1 22 #set $tval = 2
estrain@1 23 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@1 24 gunzip -c $reverse > reverse.fastq;
estrain@1 25 #set $reverse = './reverse.fastq'
estrain@1 26 gunzip -c $forward > forward.fastq;
estrain@1 27 #set $forward = './forward.fastq'
estrain@1 28 #end if
estrain@1 29 ln -s $forward ${name}_1.fastq;
estrain@1 30 ln -s $reverse ${name}_2.fastq;
estrain@1 31 #else if $reads.reads_select == 'collection'
estrain@1 32 #set $name = $reads.coll.name.replace(' ', '_')
estrain@1 33 #set $forward = $reads.coll.forward
estrain@1 34 #set $reverse = $reads.coll.reverse
estrain@1 35 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@1 36 #set $tval = 2
estrain@1 37 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@1 38 gunzip -c $reverse > reverse.fastq;
estrain@1 39 #set $reverse = './reverse.fastq'
estrain@1 40 gunzip -c $forward > forward.fastq;
estrain@1 41 #set $forward = './forward.fastq'
estrain@1 42 #end if
estrain@1 43 ln -s $forward ${name}_1.fastq;
estrain@1 44 ln -s $reverse ${name}_2.fastq;
estrain@1 45 #else
estrain@1 46 #set $name = $reads.assembly.name.replace(' ', '_')
estrain@1 47 #set $ga = $reads.assembly
estrain@1 48 #set $infile = $name + ".fasta"
estrain@1 49 ln -s $ga ${name}.fasta;
estrain@1 50 #set $tval = 4
estrain@1 51 #set $mode='k'
estrain@1 52 #end if
estrain@1 53 echo $name ;
estrain@1 54 echo "-=-=-=-=-" ;
estrain@1 55 touch output/SeqSero_log.txt ;
estrain@1 56 python $__tool_directory__/SeqSero2_package.py
estrain@1 57 -p \${GALAXY_SLOTS:-4}
estrain@1 58 -t $tval
estrain@1 59 -m $mode
estrain@1 60 -d ./output
estrain@1 61 #if $mode == 'a':
estrain@1 62 -b $maptype
estrain@1 63 #end if
estrain@1 64 -i $infile &&
estrain@1 65 echo "-=-=-=-=-" &&
estrain@1 66 cat output/SeqSero_log.txt &&
estrain@1 67 echo "-=-=-=-=-" &&
estrain@1 68 ls -lah ./output
estrain@1 69 ]]></command>
estrain@1 70 <inputs>
estrain@1 71
estrain@1 72 <conditional name="reads">
estrain@1 73 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
estrain@1 74 <option value="collection">Paired collection from your history</option>
estrain@1 75 <option value="history">Two FASTQ datasets from your history</option>
estrain@1 76 <option value="genome">Genome Assembly</option>
estrain@1 77 </param>
estrain@1 78 <when value="collection">
estrain@1 79 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
estrain@1 80 </when>
estrain@1 81 <when value="history">
estrain@1 82 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@1 83 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@1 84 </when>
estrain@1 85 <when value="genome">
estrain@1 86 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
estrain@1 87 </when>
estrain@1 88 </conditional>
estrain@1 89
estrain@1 90 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
estrain@1 91 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
estrain@1 92 <!-- <param name="numofthr" type="select" label="Number of threads">
estrain@1 93 <option value="1">1</option>
estrain@1 94 <option value="2">2</option>
estrain@1 95 <option value="3">3</option>
estrain@1 96 <option value="4">4</option> -->
estrain@1 97 <!-- </param> -->
estrain@1 98
estrain@1 99 <param label="Analysis mode" type="select" name="mode">
estrain@1 100 <option value="a">allele mode</option>
estrain@1 101 <option value="k">k-mer mode</option>
estrain@1 102 </param>
estrain@1 103
estrain@1 104 <param name="maptype" type="select" label="Algorithms for BWA mapping">
estrain@1 105 <option value="mem">mem</option>
estrain@1 106 <option value="sam">sam</option>
estrain@1 107 </param>
estrain@1 108
estrain@1 109
estrain@1 110
estrain@1 111 </inputs>
estrain@1 112 <outputs>
estrain@1 113 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/>
estrain@1 114 </outputs>
estrain@1 115 <tests>
estrain@1 116 <!-- <test>
estrain@1 117 <param name="reads_select" value="history" />
estrain@1 118 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 119 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 120 <output name="results" file="Seqsero_result.tsv" />
estrain@1 121 </test>
estrain@1 122 <test>
estrain@1 123 <param name="reads_select" value="collection" />
estrain@1 124 <param name="coll">
estrain@1 125 <collection type="paired">
estrain@1 126 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 127 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 128 </collection>
estrain@1 129 </param>
estrain@1 130 <output name="results" file="Seqsero_result.tsv" />
estrain@1 131 </test> -->
estrain@1 132 <test>
estrain@1 133 <param name="mode" value="k" />
estrain@1 134 <param name="reads_select" value="history" />
estrain@1 135 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
estrain@1 136 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
estrain@1 137 <output name="results" file="Seqsero_result_25k.tsv" />
estrain@1 138 </test>
estrain@1 139 <test>
estrain@1 140 <param name="mode" value="k" />
estrain@1 141 <param name="reads_select" value="collection" />
estrain@1 142 <param name="coll">
estrain@1 143 <collection type="paired">
estrain@1 144 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 145 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 146 </collection>
estrain@1 147 </param>
estrain@1 148 <output name="results" file="Seqsero_result_25k_coll.tsv" />
estrain@1 149 </test>
estrain@1 150 <test>
estrain@1 151 <param name="mode" value="a" />
estrain@1 152 <param name="reads_select" value="history" />
estrain@1 153 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
estrain@1 154 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
estrain@1 155 <assert_stdout>
estrain@1 156 <has_text text="predicted antigenic profile does not exist" />
estrain@1 157 </assert_stdout>
estrain@1 158 </test>
estrain@1 159 <!-- <test>
estrain@1 160 <param name="mode" value="a" />
estrain@1 161 <param name="reads_select" value="collection" />
estrain@1 162 <param name="coll">
estrain@1 163 <collection type="paired">
estrain@1 164 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 165 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1 166 </collection>
estrain@1 167 </param>
estrain@1 168 <output name="results" file="Seqsero_result_allele.tsv" />
estrain@1 169 </test> -->
estrain@1 170 </tests>
estrain@1 171 <help><![CDATA[
estrain@1 172
estrain@1 173 **Usage: SeqSero2.py**
estrain@1 174
estrain@1 175 **Algorithms for BWA mapping**
estrain@1 176
estrain@1 177 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
estrain@1 178
estrain@1 179 ]]></help>
estrain@1 180 <citations>
estrain@1 181 <citation type="bibtex">
estrain@1 182 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
estrain@1 183 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
estrain@1 184 journal={J Clin Microbiol}, publisher={ASM},
estrain@1 185 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
estrain@1 186 year={2015}, month={Max},
estrain@1 187 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
estrain@1 188 }</citation>
estrain@1 189 <citation type="bibtex">
estrain@1 190 @misc{cfsan_biostatistics_group_2017,
estrain@1 191 title={CFSAN Biostatistics Group fork of SeqSero2},
estrain@1 192 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
estrain@1 193 </citation>
estrain@1 194 </citations>
estrain@1 195
estrain@1 196 </tool>