Mercurial > repos > jpayne > seqsero_v2

annotate seqsero.xml @ 15:1d6702e0bffd

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author estrain
date Wed, 01 Mar 2023 13:20:59 -0500
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estrain@15 1 <tool id="seqsero_v2" name="SeqSero2 v1.2.1" version="8">
estrain@15 2 <description>Salmonella serotype prediction</description>
estrain@15 3 <macros>
estrain@15 4 <token name="@VERSION@">1.2.1</token>
estrain@15 5 </macros>
estrain@15 6 <requirements>
estrain@15 7 <requirement type="package" version="@VERSION@">seqsero2</requirement>
estrain@15 8 </requirements>
estrain@15 9 <command detect_errors="exit_code"><![CDATA[
estrain@15 10 echo "SeqSero2 v1.2.1";
estrain@15 11 mkdir ./output;
estrain@15 12
estrain@15 13 #if $reads.reads_select == 'history'
estrain@15 14 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@15 15 #set $forward = $reads.forward
estrain@15 16 #set $reverse = $reads.reverse
estrain@15 17 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@15 18 #set $tval = 2
estrain@15 19 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@15 20 gunzip -c $reverse > reverse.fastq;
estrain@15 21 #set $reverse = './reverse.fastq'
estrain@15 22 gunzip -c $forward > forward.fastq;
estrain@15 23 #set $forward = './forward.fastq'
estrain@15 24 #end if
estrain@15 25 ln -s $forward ${name}_1.fastq;
estrain@15 26 ln -s $reverse ${name}_2.fastq;
estrain@15 27 #else if $reads.reads_select == 'collection'
estrain@15 28 #set $name = $reads.coll.name.replace(' ', '_')
estrain@15 29 #set $forward = $reads.coll.forward
estrain@15 30 #set $reverse = $reads.coll.reverse
estrain@15 31 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@15 32 #set $tval = 2
estrain@15 33 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@15 34 gunzip -c $reverse > reverse.fastq;
estrain@15 35 #set $reverse = './reverse.fastq'
estrain@15 36 gunzip -c $forward > forward.fastq;
estrain@15 37 #set $forward = './forward.fastq'
estrain@15 38 #end if
estrain@15 39 ln -s $forward ${name}_1.fastq;
estrain@15 40 ln -s $reverse ${name}_2.fastq;
estrain@15 41 #else
estrain@15 42 #set $name = $reads.assembly.name.replace(' ', '_')
estrain@15 43 #set $ga = $reads.assembly
estrain@15 44 #set $infile = $name + ".fasta"
estrain@15 45 ln -s $ga ${name}.fasta;
estrain@15 46 #set $tval = 4
estrain@15 47 #set $mode='k'
estrain@15 48 #end if
estrain@15 49 echo $name ;
estrain@15 50 echo "-=-=-=-=-" ;
estrain@15 51 touch output/SeqSero_log.txt ;
estrain@15 52 SeqSero2_package.py
estrain@15 53 -p \${GALAXY_SLOTS:-1}
estrain@15 54 -t $tval
estrain@15 55 -m $mode
estrain@15 56 -d ./output
estrain@15 57 #if $mode == 'a':
estrain@15 58 -b $maptype
estrain@15 59 #end if
estrain@15 60 -i $infile &&
estrain@15 61 echo "-=-=-=-=-" &&
estrain@15 62 cat output/SeqSero_log.txt &&
estrain@15 63 echo "-=-=-=-=-" &&
estrain@15 64 ls -lah ./output
estrain@15 65 ]]></command>
estrain@15 66 <inputs>
estrain@15 67
estrain@15 68 <conditional name="reads">
estrain@15 69 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
estrain@15 70 <option value="collection">Paired collection from your history</option>
estrain@15 71 <option value="history">Two FASTQ datasets from your history</option>
estrain@15 72 <option value="genome">Genome Assembly</option>
estrain@15 73 </param>
estrain@15 74 <when value="collection">
estrain@15 75 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
estrain@15 76 </when>
estrain@15 77 <when value="history">
estrain@15 78 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@15 79 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@15 80 </when>
estrain@15 81 <when value="genome">
estrain@15 82 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
estrain@15 83 </when>
estrain@15 84 </conditional>
estrain@15 85
estrain@15 86 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
estrain@15 87 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
estrain@15 88 <!-- <param name="numofthr" type="select" label="Number of threads">
estrain@15 89 <option value="1">1</option>
estrain@15 90 <option value="2">2</option>
estrain@15 91 <option value="3">3</option>
estrain@15 92 <option value="4">4</option> -->
estrain@15 93 <!-- </param> -->
estrain@15 94
estrain@15 95 <param label="Analysis mode" type="select" name="mode">
estrain@15 96 <option value="a">allele mode</option>
estrain@15 97 <option value="k">k-mer mode</option>
estrain@15 98 </param>
estrain@15 99
estrain@15 100 <param name="maptype" type="select" label="Algorithms for BWA mapping">
estrain@15 101 <option value="mem">mem</option>
estrain@15 102 <option value="sam">sam</option>
estrain@15 103 </param>
estrain@15 104
estrain@15 105
estrain@15 106
estrain@15 107 </inputs>
estrain@15 108 <outputs>
estrain@15 109 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/>
estrain@15 110 </outputs>
estrain@15 111 <tests>
estrain@15 112 <!-- <test>
estrain@15 113 <param name="reads_select" value="history" />
estrain@15 114 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 115 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 116 <output name="results" file="Seqsero_result.tsv" />
estrain@15 117 </test>
estrain@15 118 <test>
estrain@15 119 <param name="reads_select" value="collection" />
estrain@15 120 <param name="coll">
estrain@15 121 <collection type="paired">
estrain@15 122 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 123 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 124 </collection>
estrain@15 125 </param>
estrain@15 126 <output name="results" file="Seqsero_result.tsv" />
estrain@15 127 </test> -->
estrain@15 128 <test>
estrain@15 129 <param name="mode" value="k" />
estrain@15 130 <param name="reads_select" value="history" />
estrain@15 131 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
estrain@15 132 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
estrain@15 133 <output name="results" file="Seqsero_result_25k.tsv" />
estrain@15 134 </test>
estrain@15 135 <test>
estrain@15 136 <param name="mode" value="k" />
estrain@15 137 <param name="reads_select" value="collection" />
estrain@15 138 <param name="coll">
estrain@15 139 <collection type="paired">
estrain@15 140 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 141 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 142 </collection>
estrain@15 143 </param>
estrain@15 144 <output name="results" file="Seqsero_result_25k_coll.tsv" />
estrain@15 145 </test>
estrain@15 146 <test>
estrain@15 147 <param name="mode" value="a" />
estrain@15 148 <param name="reads_select" value="history" />
estrain@15 149 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
estrain@15 150 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
estrain@15 151 <assert_stdout>
estrain@15 152 <has_text text="predicted antigenic profile does not exist" />
estrain@15 153 </assert_stdout>
estrain@15 154 </test>
estrain@15 155 <!-- <test>
estrain@15 156 <param name="mode" value="a" />
estrain@15 157 <param name="reads_select" value="collection" />
estrain@15 158 <param name="coll">
estrain@15 159 <collection type="paired">
estrain@15 160 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 161 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@15 162 </collection>
estrain@15 163 </param>
estrain@15 164 <output name="results" file="Seqsero_result_allele.tsv" />
estrain@15 165 </test> -->
estrain@15 166 </tests>
estrain@15 167 <help><![CDATA[
estrain@15 168
estrain@15 169 **Usage: SeqSero2.py**
estrain@15 170
estrain@15 171 **Algorithms for BWA mapping**
estrain@15 172
estrain@15 173 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
estrain@15 174
estrain@15 175 ]]></help>
estrain@15 176 <citations>
estrain@15 177 <citation type="bibtex">
estrain@15 178 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
estrain@15 179 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
estrain@15 180 journal={J Clin Microbiol}, publisher={ASM},
estrain@15 181 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
estrain@15 182 year={2015}, month={Max},
estrain@15 183 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
estrain@15 184 }</citation>
estrain@15 185 <citation type="bibtex">
estrain@15 186 @misc{cfsan_biostatistics_group_2017,
estrain@15 187 title={CFSAN Biostatistics Group fork of SeqSero2},
estrain@15 188 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
estrain@15 189 </citation>
estrain@15 190 </citations>
estrain@15 191
estrain@15 192 </tool>