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annotate seqsero2.xml @ 35:b99f3a65254d

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author estrain
date Sat, 07 Sep 2019 15:27:43 -0400
parents 6d8f3c66a836
children 2fb62709dc5e
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estrain@8 1 <tool id="seqsero2_v1_0_1" name="SeqSero 2" version="1.0.1">
estrain@8 2 <description>Salmonella serotype prediction</description>
estrain@8 3 <requirements>
estrain@35 4 <requirement type="package">biopython</requirement>
estrain@35 5 <requirement type="package">blast</requirement>
estrain@35 6 <requirement type="package">samtools</requirement>
estrain@35 7 <requirement type="package">sra-tools</requirement>
estrain@35 8 <requirement type="package">bwa</requirement>
estrain@35 9 <requirement type="package">spades</requirement>
estrain@35 10 <requirement type="package">bedtools</requirement>
estrain@8 11 </requirements>
estrain@8 12 <command detect_errors="exit_code"><![CDATA[
estrain@8 13 echo "SeqSero 2 v. 1.0.1" ;
estrain@27 14 mkdir ./output;
estrain@20 15
estrain@8 16 #if $reads.reads_select == 'history'
estrain@27 17 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@27 18 #set $forward = $reads.forward
estrain@27 19 #set $reverse = $reads.reverse
estrain@8 20 #else
estrain@27 21 #set $name = $reads.coll.name.replace(' ', '_')
estrain@27 22 #set $forward = $reads.coll.forward
estrain@27 23 #set $reverse = $reads.coll.reverse
estrain@8 24 #end if
estrain@27 25 echo $name ;
estrain@27 26 echo "-=-=-=-=-" ;
estrain@8 27 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@8 28 gunzip -c $forward > forward.fastq;
estrain@27 29 #set $forward = './forward.fastq'
estrain@8 30 #end if
estrain@8 31 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@8 32 gunzip -c $reverse > reverse.fastq;
estrain@27 33 #set $reverse = './reverse.fastq'
estrain@8 34 #end if
estrain@27 35 ln -s $forward ${name}_1.fastq;
estrain@27 36 ln -s $reverse ${name}_2.fastq;
estrain@27 37 touch output/SeqSero_log.txt ;
estrain@35 38 python3 $__tool_directory__/SeqSero2_package.py
estrain@8 39 -p \${GALAXY_SLOTS:-4}
estrain@8 40 -t 2
estrain@8 41 -m $mode
estrain@8 42 -d ./output
estrain@8 43 #if $mode == 'a':
estrain@8 44 -b $maptype
estrain@8 45 #end if
estrain@8 46 -i ${name}_1.fastq ${name}_2.fastq &&
estrain@8 47 echo "-=-=-=-=-" &&
estrain@8 48 cat output/SeqSero_log.txt &&
estrain@8 49 echo "-=-=-=-=-" &&
estrain@8 50 ls -lah ./output
estrain@8 51 ]]></command>
estrain@8 52 <inputs>
estrain@8 53
estrain@8 54 <conditional name="reads">
estrain@8 55 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
estrain@8 56 <option value="collection">Paired collection from your history</option>
estrain@8 57 <option value="history">Two FASTQ datasets from your history</option>
estrain@8 58 </param>
estrain@8 59 <when value="collection">
estrain@8 60 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
estrain@8 61 </when>
estrain@8 62 <when value="history">
estrain@8 63 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@8 64 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@8 65 </when>
estrain@8 66 </conditional>
estrain@8 67
estrain@8 68 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
estrain@8 69 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
estrain@8 70 <!-- <param name="numofthr" type="select" label="Number of threads">
estrain@8 71 <option value="1">1</option>
estrain@8 72 <option value="2">2</option>
estrain@8 73 <option value="3">3</option>
estrain@8 74 <option value="4">4</option> -->
estrain@8 75 <!-- </param> -->
estrain@8 76
estrain@8 77 <param label="Analysis mode" type="select" name="mode">
estrain@8 78 <option value="a">allele mode</option>
estrain@8 79 <option value="k">k-mer mode</option>
estrain@8 80 </param>
estrain@8 81
estrain@8 82 <param name="maptype" type="select" label="Algorithms for BWA mapping">
estrain@8 83 <option value="mem">mem</option>
estrain@8 84 <option value="sam">sam</option>
estrain@8 85 </param>
estrain@8 86
estrain@8 87
estrain@8 88
estrain@8 89 </inputs>
estrain@8 90 <outputs>
estrain@12 91 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/>
estrain@8 92 </outputs>
estrain@8 93 <tests>
estrain@8 94 <!-- <test>
estrain@8 95 <param name="reads_select" value="history" />
estrain@8 96 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 97 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 98 <output name="results" file="Seqsero_result.tsv" />
estrain@8 99 </test>
estrain@8 100 <test>
estrain@8 101 <param name="reads_select" value="collection" />
estrain@8 102 <param name="coll">
estrain@8 103 <collection type="paired">
estrain@8 104 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 105 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 106 </collection>
estrain@8 107 </param>
estrain@8 108 <output name="results" file="Seqsero_result.tsv" />
estrain@8 109 </test> -->
estrain@8 110 <test>
estrain@8 111 <param name="mode" value="k" />
estrain@8 112 <param name="reads_select" value="history" />
estrain@8 113 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
estrain@8 114 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
estrain@8 115 <output name="results" file="Seqsero_result_25k.tsv" />
estrain@8 116 </test>
estrain@8 117 <test>
estrain@8 118 <param name="mode" value="k" />
estrain@8 119 <param name="reads_select" value="collection" />
estrain@8 120 <param name="coll">
estrain@8 121 <collection type="paired">
estrain@8 122 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 123 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 124 </collection>
estrain@8 125 </param>
estrain@8 126 <output name="results" file="Seqsero_result_25k_coll.tsv" />
estrain@8 127 </test>
estrain@8 128 <test>
estrain@8 129 <param name="mode" value="a" />
estrain@8 130 <param name="reads_select" value="history" />
estrain@8 131 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
estrain@8 132 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
estrain@8 133 <assert_stdout>
estrain@8 134 <has_text text="predicted antigenic profile does not exist" />
estrain@8 135 </assert_stdout>
estrain@8 136 </test>
estrain@8 137 <!-- <test>
estrain@8 138 <param name="mode" value="a" />
estrain@8 139 <param name="reads_select" value="collection" />
estrain@8 140 <param name="coll">
estrain@8 141 <collection type="paired">
estrain@8 142 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 143 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 144 </collection>
estrain@8 145 </param>
estrain@8 146 <output name="results" file="Seqsero_result_allele.tsv" />
estrain@8 147 </test> -->
estrain@8 148 </tests>
estrain@8 149 <help><![CDATA[
estrain@8 150
estrain@8 151 **Usage: SeqSero2.py**
estrain@8 152
estrain@8 153 **Algorithms for BWA mapping**
estrain@8 154
estrain@8 155 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
estrain@8 156
estrain@8 157 ]]></help>
estrain@8 158 <citations>
estrain@8 159 <citation type="bibtex">
estrain@8 160 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
estrain@8 161 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
estrain@8 162 journal={J Clin Microbiol}, publisher={ASM},
estrain@8 163 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
estrain@8 164 year={2015}, month={Max},
estrain@8 165 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
estrain@8 166 }</citation>
estrain@8 167 <citation type="bibtex">
estrain@8 168 @misc{cfsan_biostatistics_group_2017,
estrain@8 169 title={CFSAN Biostatistics Group fork of SeqSero2},
estrain@8 170 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
estrain@8 171 </citation>
estrain@8 172 </citations>
estrain@8 173
estrain@8 174 </tool>