Mercurial > repos > jpayne > seqsero_v2

annotate seqsero2.xml @ 18:a573df21536d tip

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author jpayne
date Wed, 26 Mar 2025 00:28:55 -0400
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jpayne@18 1 <tool id="seqsero_v2" name="SeqSero2 v1.3.1" version="9">
jpayne@0 2 <description>Salmonella serotype prediction</description>
estrain@14 3 <macros>
jpayne@17 4 <token name="@VERSION@">1.3.1</token>
estrain@14 5 </macros>
jpayne@0 6 <requirements>
estrain@14 7 <requirement type="package" version="@VERSION@">seqsero2</requirement>
jpayne@0 8 </requirements>
jpayne@0 9 <command detect_errors="exit_code"><![CDATA[
estrain@14 10 mkdir ./output;
estrain@14 11
jpayne@3 12 #if $reads.reads_select == 'history'
estrain@14 13 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@14 14 #set $forward = $reads.forward
estrain@14 15 #set $reverse = $reads.reverse
estrain@14 16 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@14 17 #set $tval = 2
estrain@14 18 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@14 19 gunzip -c $reverse > reverse.fastq;
estrain@14 20 #set $reverse = './reverse.fastq'
estrain@14 21 gunzip -c $forward > forward.fastq;
estrain@14 22 #set $forward = './forward.fastq'
estrain@14 23 #end if
jpayne@3 24 ln -s $forward ${name}_1.fastq;
jpayne@3 25 ln -s $reverse ${name}_2.fastq;
estrain@14 26 #else if $reads.reads_select == 'collection'
estrain@14 27 #set $name = $reads.coll.name.replace(' ', '_')
estrain@14 28 #set $forward = $reads.coll.forward
estrain@14 29 #set $reverse = $reads.coll.reverse
estrain@14 30 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@14 31 #set $tval = 2
estrain@14 32 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@14 33 gunzip -c $reverse > reverse.fastq;
estrain@14 34 #set $reverse = './reverse.fastq'
estrain@14 35 gunzip -c $forward > forward.fastq;
estrain@14 36 #set $forward = './forward.fastq'
estrain@14 37 #end if
estrain@14 38 ln -s $forward ${name}_1.fastq;
estrain@14 39 ln -s $reverse ${name}_2.fastq;
estrain@14 40 #else
estrain@14 41 #set $name = $reads.assembly.name.replace(' ', '_')
estrain@14 42 #set $ga = $reads.assembly
estrain@14 43 #set $infile = $name + ".fasta"
estrain@14 44 ln -s $ga ${name}.fasta;
estrain@14 45 #set $tval = 4
estrain@14 46 #set $mode='k'
estrain@14 47 #end if
estrain@14 48 echo $name ;
estrain@14 49 echo "-=-=-=-=-" ;
estrain@14 50 touch output/SeqSero_log.txt ;
jpayne@17 51 SeqSero2_package.py --version ;
jpayne@17 52 echo "-=-=-=-=-" ;
estrain@14 53 SeqSero2_package.py
estrain@14 54 -p \${GALAXY_SLOTS:-1}
estrain@14 55 -t $tval
jpayne@2 56 -m $mode
jpayne@2 57 -d ./output
jpayne@2 58 #if $mode == 'a':
jpayne@2 59 -b $maptype
jpayne@2 60 #end if
estrain@14 61 -i $infile &&
jpayne@2 62 echo "-=-=-=-=-" &&
jpayne@2 63 cat output/SeqSero_log.txt &&
jpayne@2 64 echo "-=-=-=-=-" &&
jpayne@2 65 ls -lah ./output
jpayne@0 66 ]]></command>
jpayne@0 67 <inputs>
jpayne@0 68
jpayne@0 69 <conditional name="reads">
estrain@14 70 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
jpayne@0 71 <option value="collection">Paired collection from your history</option>
jpayne@0 72 <option value="history">Two FASTQ datasets from your history</option>
estrain@14 73 <option value="genome">Genome Assembly</option>
jpayne@0 74 </param>
jpayne@0 75 <when value="collection">
jpayne@0 76 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
jpayne@0 77 </when>
jpayne@0 78 <when value="history">
jpayne@0 79 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 80 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 81 </when>
estrain@14 82 <when value="genome">
estrain@14 83 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
estrain@14 84 </when>
jpayne@0 85 </conditional>
jpayne@0 86
jpayne@0 87 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
jpayne@0 88 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
jpayne@0 89 <!-- <param name="numofthr" type="select" label="Number of threads">
jpayne@0 90 <option value="1">1</option>
jpayne@0 91 <option value="2">2</option>
jpayne@0 92 <option value="3">3</option>
jpayne@0 93 <option value="4">4</option> -->
jpayne@0 94 <!-- </param> -->
jpayne@2 95
jpayne@2 96 <param label="Analysis mode" type="select" name="mode">
estrain@14 97 <option value="a">allele mode</option>
estrain@14 98 <option value="k">k-mer mode</option>
jpayne@2 99 </param>
jpayne@2 100
jpayne@2 101 <param name="maptype" type="select" label="Algorithms for BWA mapping">
jpayne@0 102 <option value="mem">mem</option>
jpayne@0 103 <option value="sam">sam</option>
jpayne@0 104 </param>
jpayne@2 105
jpayne@0 106
jpayne@0 107
jpayne@0 108 </inputs>
jpayne@0 109 <outputs>
jpayne@17 110 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv" />
jpayne@0 111 </outputs>
jpayne@0 112 <tests>
jpayne@1 113 <!-- <test>
jpayne@1 114 <param name="reads_select" value="history" />
jpayne@1 115 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 116 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 117 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 118 </test>
jpayne@0 119 <test>
jpayne@1 120 <param name="reads_select" value="collection" />
jpayne@1 121 <param name="coll">
jpayne@1 122 <collection type="paired">
jpayne@1 123 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 124 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 125 </collection>
jpayne@1 126 </param>
jpayne@1 127 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 128 </test> -->
jpayne@1 129 <test>
jpayne@1 130 <param name="mode" value="k" />
jpayne@0 131 <param name="reads_select" value="history" />
jpayne@3 132 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
jpayne@3 133 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
jpayne@1 134 <output name="results" file="Seqsero_result_25k.tsv" />
jpayne@0 135 </test>
jpayne@0 136 <test>
jpayne@1 137 <param name="mode" value="k" />
jpayne@0 138 <param name="reads_select" value="collection" />
jpayne@0 139 <param name="coll">
jpayne@0 140 <collection type="paired">
jpayne@0 141 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 142 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 143 </collection>
jpayne@0 144 </param>
jpayne@1 145 <output name="results" file="Seqsero_result_25k_coll.tsv" />
jpayne@0 146 </test>
jpayne@11 147 <test>
jpayne@11 148 <param name="mode" value="a" />
jpayne@11 149 <param name="reads_select" value="history" />
jpayne@12 150 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
jpayne@12 151 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
jpayne@12 152 <assert_stdout>
jpayne@17 153 <has_text text="input genome cannot be identified as Salmonella" />
jpayne@12 154 </assert_stdout>
jpayne@11 155 </test>
jpayne@1 156 <!-- <test>
jpayne@1 157 <param name="mode" value="a" />
jpayne@1 158 <param name="reads_select" value="collection" />
jpayne@1 159 <param name="coll">
jpayne@1 160 <collection type="paired">
jpayne@1 161 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 162 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 163 </collection>
jpayne@1 164 </param>
jpayne@1 165 <output name="results" file="Seqsero_result_allele.tsv" />
jpayne@1 166 </test> -->
jpayne@0 167 </tests>
jpayne@0 168 <help><![CDATA[
jpayne@0 169
jpayne@0 170 **Usage: SeqSero2.py**
jpayne@0 171
jpayne@0 172 **Algorithms for BWA mapping**
jpayne@0 173
jpayne@0 174 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
jpayne@0 175
jpayne@0 176 ]]></help>
jpayne@0 177 <citations>
jpayne@0 178 <citation type="bibtex">
jpayne@0 179 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
jpayne@0 180 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
jpayne@0 181 journal={J Clin Microbiol}, publisher={ASM},
jpayne@0 182 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
jpayne@0 183 year={2015}, month={Max},
jpayne@0 184 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
jpayne@0 185 }</citation>
jpayne@5 186 <citation type="bibtex">
jpayne@5 187 @misc{cfsan_biostatistics_group_2017,
jpayne@5 188 title={CFSAN Biostatistics Group fork of SeqSero2},
jpayne@5 189 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
jpayne@5 190 </citation>
jpayne@0 191 </citations>
jpayne@0 192
jpayne@0 193 </tool>