Mercurial > repos > jpayne > seqsero_v2

annotate seqsero2.xml @ 14:496f5f2b5e75

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author estrain
date Tue, 14 Feb 2023 12:11:27 -0500
parents 3513b93ebe6a
children 3b6d5b60968f
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estrain@14 1 <tool id="seqsero2v111" name="SeqSero2 v1.2.1" version="8">
jpayne@0 2 <description>Salmonella serotype prediction</description>
estrain@14 3 <macros>
estrain@14 4 <token name="@VERSION@">1.2.1</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 echo "SeqSero2 v1.2.1";
estrain@14 11 mkdir ./output;
estrain@14 12
jpayne@3 13 #if $reads.reads_select == 'history'
estrain@14 14 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@14 15 #set $forward = $reads.forward
estrain@14 16 #set $reverse = $reads.reverse
estrain@14 17 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@14 18 #set $tval = 2
estrain@14 19 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@14 20 gunzip -c $reverse > reverse.fastq;
estrain@14 21 #set $reverse = './reverse.fastq'
estrain@14 22 gunzip -c $forward > forward.fastq;
estrain@14 23 #set $forward = './forward.fastq'
estrain@14 24 #end if
jpayne@3 25 ln -s $forward ${name}_1.fastq;
jpayne@3 26 ln -s $reverse ${name}_2.fastq;
estrain@14 27 #else if $reads.reads_select == 'collection'
estrain@14 28 #set $name = $reads.coll.name.replace(' ', '_')
estrain@14 29 #set $forward = $reads.coll.forward
estrain@14 30 #set $reverse = $reads.coll.reverse
estrain@14 31 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
estrain@14 32 #set $tval = 2
estrain@14 33 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@14 34 gunzip -c $reverse > reverse.fastq;
estrain@14 35 #set $reverse = './reverse.fastq'
estrain@14 36 gunzip -c $forward > forward.fastq;
estrain@14 37 #set $forward = './forward.fastq'
estrain@14 38 #end if
estrain@14 39 ln -s $forward ${name}_1.fastq;
estrain@14 40 ln -s $reverse ${name}_2.fastq;
estrain@14 41 #else
estrain@14 42 #set $name = $reads.assembly.name.replace(' ', '_')
estrain@14 43 #set $ga = $reads.assembly
estrain@14 44 #set $infile = $name + ".fasta"
estrain@14 45 ln -s $ga ${name}.fasta;
estrain@14 46 #set $tval = 4
estrain@14 47 #set $mode='k'
estrain@14 48 #end if
estrain@14 49 echo $name ;
estrain@14 50 echo "-=-=-=-=-" ;
estrain@14 51 touch output/SeqSero_log.txt ;
estrain@14 52 SeqSero2_package.py
estrain@14 53 -p \${GALAXY_SLOTS:-1}
estrain@14 54 -t $tval
jpayne@2 55 -m $mode
jpayne@2 56 -d ./output
jpayne@2 57 #if $mode == 'a':
jpayne@2 58 -b $maptype
jpayne@2 59 #end if
estrain@14 60 -i $infile &&
jpayne@2 61 echo "-=-=-=-=-" &&
jpayne@2 62 cat output/SeqSero_log.txt &&
jpayne@2 63 echo "-=-=-=-=-" &&
jpayne@2 64 ls -lah ./output
jpayne@0 65 ]]></command>
jpayne@0 66 <inputs>
jpayne@0 67
jpayne@0 68 <conditional name="reads">
estrain@14 69 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
jpayne@0 70 <option value="collection">Paired collection from your history</option>
jpayne@0 71 <option value="history">Two FASTQ datasets from your history</option>
estrain@14 72 <option value="genome">Genome Assembly</option>
jpayne@0 73 </param>
jpayne@0 74 <when value="collection">
jpayne@0 75 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
jpayne@0 76 </when>
jpayne@0 77 <when value="history">
jpayne@0 78 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 79 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0 80 </when>
estrain@14 81 <when value="genome">
estrain@14 82 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
estrain@14 83 </when>
jpayne@0 84 </conditional>
jpayne@0 85
jpayne@0 86 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
jpayne@0 87 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
jpayne@0 88 <!-- <param name="numofthr" type="select" label="Number of threads">
jpayne@0 89 <option value="1">1</option>
jpayne@0 90 <option value="2">2</option>
jpayne@0 91 <option value="3">3</option>
jpayne@0 92 <option value="4">4</option> -->
jpayne@0 93 <!-- </param> -->
jpayne@2 94
jpayne@2 95 <param label="Analysis mode" type="select" name="mode">
estrain@14 96 <option value="a">allele mode</option>
estrain@14 97 <option value="k">k-mer mode</option>
jpayne@2 98 </param>
jpayne@2 99
jpayne@2 100 <param name="maptype" type="select" label="Algorithms for BWA mapping">
jpayne@0 101 <option value="mem">mem</option>
jpayne@0 102 <option value="sam">sam</option>
jpayne@0 103 </param>
jpayne@2 104
jpayne@0 105
jpayne@0 106
jpayne@0 107 </inputs>
jpayne@0 108 <outputs>
estrain@14 109 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/>
jpayne@0 110 </outputs>
jpayne@0 111 <tests>
jpayne@1 112 <!-- <test>
jpayne@1 113 <param name="reads_select" value="history" />
jpayne@1 114 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 115 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 116 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 117 </test>
jpayne@0 118 <test>
jpayne@1 119 <param name="reads_select" value="collection" />
jpayne@1 120 <param name="coll">
jpayne@1 121 <collection type="paired">
jpayne@1 122 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 123 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 124 </collection>
jpayne@1 125 </param>
jpayne@1 126 <output name="results" file="Seqsero_result.tsv" />
jpayne@1 127 </test> -->
jpayne@1 128 <test>
jpayne@1 129 <param name="mode" value="k" />
jpayne@0 130 <param name="reads_select" value="history" />
jpayne@3 131 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
jpayne@3 132 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
jpayne@1 133 <output name="results" file="Seqsero_result_25k.tsv" />
jpayne@0 134 </test>
jpayne@0 135 <test>
jpayne@1 136 <param name="mode" value="k" />
jpayne@0 137 <param name="reads_select" value="collection" />
jpayne@0 138 <param name="coll">
jpayne@0 139 <collection type="paired">
jpayne@0 140 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 141 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0 142 </collection>
jpayne@0 143 </param>
jpayne@1 144 <output name="results" file="Seqsero_result_25k_coll.tsv" />
jpayne@0 145 </test>
jpayne@11 146 <test>
jpayne@11 147 <param name="mode" value="a" />
jpayne@11 148 <param name="reads_select" value="history" />
jpayne@12 149 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
jpayne@12 150 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
jpayne@12 151 <assert_stdout>
estrain@14 152 <has_text text="predicted antigenic profile does not exist" />
jpayne@12 153 </assert_stdout>
jpayne@11 154 </test>
jpayne@1 155 <!-- <test>
jpayne@1 156 <param name="mode" value="a" />
jpayne@1 157 <param name="reads_select" value="collection" />
jpayne@1 158 <param name="coll">
jpayne@1 159 <collection type="paired">
jpayne@1 160 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 161 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1 162 </collection>
jpayne@1 163 </param>
jpayne@1 164 <output name="results" file="Seqsero_result_allele.tsv" />
jpayne@1 165 </test> -->
jpayne@0 166 </tests>
jpayne@0 167 <help><![CDATA[
jpayne@0 168
jpayne@0 169 **Usage: SeqSero2.py**
jpayne@0 170
jpayne@0 171 **Algorithms for BWA mapping**
jpayne@0 172
jpayne@0 173 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
jpayne@0 174
jpayne@0 175 ]]></help>
jpayne@0 176 <citations>
jpayne@0 177 <citation type="bibtex">
jpayne@0 178 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
jpayne@0 179 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
jpayne@0 180 journal={J Clin Microbiol}, publisher={ASM},
jpayne@0 181 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
jpayne@0 182 year={2015}, month={Max},
jpayne@0 183 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
jpayne@0 184 }</citation>
jpayne@5 185 <citation type="bibtex">
jpayne@5 186 @misc{cfsan_biostatistics_group_2017,
jpayne@5 187 title={CFSAN Biostatistics Group fork of SeqSero2},
jpayne@5 188 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
jpayne@5 189 </citation>
jpayne@0 190 </citations>
jpayne@0 191
jpayne@0 192 </tool>