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annotate seqsero2.xml @ 26:2bc92eaf2844

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author estrain
date Sat, 07 Sep 2019 14:13:54 -0400
parents 55d2ec45737f
children 4a709def2980
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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@8 4 <requirement type="package" version="3.6">python</requirement>
estrain@12 5 <requirement type="package" version="1.74">biopython</requirement>
estrain@8 6 <requirement type="package" version="2.7.1">blast</requirement>
estrain@8 7 <requirement type="package" version="1.9">samtools</requirement>
estrain@8 8 <requirement type="package" version="2.9.1">sra-tools</requirement>
estrain@8 9 <requirement type="package" version="0.7.17">bwa</requirement>
estrain@8 10 <requirement type="package" version="3.13.1">spades</requirement>
estrain@8 11 <requirement type="package" version="2.27.1">bedtools</requirement>
estrain@8 12 </requirements>
estrain@8 13 <command detect_errors="exit_code"><![CDATA[
estrain@8 14 echo "SeqSero 2 v. 1.0.1" ;
estrain@20 15
estrain@8 16 #if $reads.reads_select == 'history'
estrain@8 17 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@8 18 #set $forward = $reads.forward
estrain@8 19 #set $reverse = $reads.reverse
estrain@8 20 #else
estrain@8 21 #set $name = $reads.coll.name.replace(' ', '_')
estrain@8 22 #set $forward = $reads.coll.forward
estrain@8 23 #set $reverse = $reads.coll.reverse
estrain@8 24 #end if
estrain@8 25 echo $name ;
estrain@8 26 echo "-=-=-=-=-" ;
estrain@8 27 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@8 28 gunzip -c $forward > forward.fastq;
estrain@8 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@8 33 #set $reverse = './reverse.fastq'
estrain@8 34 #end if
estrain@8 35 ln -s $forward ${name}_1.fastq;
estrain@8 36 ln -s $reverse ${name}_2.fastq;
estrain@8 37 mkdir ./output;
estrain@8 38 touch output/SeqSero_log.txt ;
estrain@25 39 python $__tool_directory__/SalmID.py -i ${name}_1.fastq > salmid_output.txt;
estrain@8 40 python $__tool_directory__/SeqSero2_package.py
estrain@8 41 -p \${GALAXY_SLOTS:-4}
estrain@8 42 -t 2
estrain@8 43 -m $mode
estrain@8 44 -d ./output
estrain@8 45 #if $mode == 'a':
estrain@8 46 -b $maptype
estrain@8 47 #end if
estrain@8 48 -i ${name}_1.fastq ${name}_2.fastq &&
estrain@8 49 echo "-=-=-=-=-" &&
estrain@8 50 cat output/SeqSero_log.txt &&
estrain@8 51 echo "-=-=-=-=-" &&
estrain@8 52 ls -lah ./output
estrain@8 53 ]]></command>
estrain@8 54 <inputs>
estrain@8 55
estrain@8 56 <conditional name="reads">
estrain@8 57 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
estrain@8 58 <option value="collection">Paired collection from your history</option>
estrain@8 59 <option value="history">Two FASTQ datasets from your history</option>
estrain@8 60 </param>
estrain@8 61 <when value="collection">
estrain@8 62 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
estrain@8 63 </when>
estrain@8 64 <when value="history">
estrain@8 65 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@8 66 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@8 67 </when>
estrain@8 68 </conditional>
estrain@8 69
estrain@8 70 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
estrain@8 71 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
estrain@8 72 <!-- <param name="numofthr" type="select" label="Number of threads">
estrain@8 73 <option value="1">1</option>
estrain@8 74 <option value="2">2</option>
estrain@8 75 <option value="3">3</option>
estrain@8 76 <option value="4">4</option> -->
estrain@8 77 <!-- </param> -->
estrain@8 78
estrain@8 79 <param label="Analysis mode" type="select" name="mode">
estrain@8 80 <option value="a">allele mode</option>
estrain@8 81 <option value="k">k-mer mode</option>
estrain@8 82 </param>
estrain@8 83
estrain@8 84 <param name="maptype" type="select" label="Algorithms for BWA mapping">
estrain@8 85 <option value="mem">mem</option>
estrain@8 86 <option value="sam">sam</option>
estrain@8 87 </param>
estrain@8 88
estrain@8 89
estrain@8 90
estrain@8 91 </inputs>
estrain@8 92 <outputs>
estrain@12 93 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/>
estrain@8 94 </outputs>
estrain@8 95 <tests>
estrain@8 96 <!-- <test>
estrain@8 97 <param name="reads_select" value="history" />
estrain@8 98 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 99 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 100 <output name="results" file="Seqsero_result.tsv" />
estrain@8 101 </test>
estrain@8 102 <test>
estrain@8 103 <param name="reads_select" value="collection" />
estrain@8 104 <param name="coll">
estrain@8 105 <collection type="paired">
estrain@8 106 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 107 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 108 </collection>
estrain@8 109 </param>
estrain@8 110 <output name="results" file="Seqsero_result.tsv" />
estrain@8 111 </test> -->
estrain@8 112 <test>
estrain@8 113 <param name="mode" value="k" />
estrain@8 114 <param name="reads_select" value="history" />
estrain@8 115 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
estrain@8 116 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
estrain@8 117 <output name="results" file="Seqsero_result_25k.tsv" />
estrain@8 118 </test>
estrain@8 119 <test>
estrain@8 120 <param name="mode" value="k" />
estrain@8 121 <param name="reads_select" value="collection" />
estrain@8 122 <param name="coll">
estrain@8 123 <collection type="paired">
estrain@8 124 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 125 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 126 </collection>
estrain@8 127 </param>
estrain@8 128 <output name="results" file="Seqsero_result_25k_coll.tsv" />
estrain@8 129 </test>
estrain@8 130 <test>
estrain@8 131 <param name="mode" value="a" />
estrain@8 132 <param name="reads_select" value="history" />
estrain@8 133 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
estrain@8 134 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
estrain@8 135 <assert_stdout>
estrain@8 136 <has_text text="predicted antigenic profile does not exist" />
estrain@8 137 </assert_stdout>
estrain@8 138 </test>
estrain@8 139 <!-- <test>
estrain@8 140 <param name="mode" value="a" />
estrain@8 141 <param name="reads_select" value="collection" />
estrain@8 142 <param name="coll">
estrain@8 143 <collection type="paired">
estrain@8 144 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 145 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@8 146 </collection>
estrain@8 147 </param>
estrain@8 148 <output name="results" file="Seqsero_result_allele.tsv" />
estrain@8 149 </test> -->
estrain@8 150 </tests>
estrain@8 151 <help><![CDATA[
estrain@8 152
estrain@8 153 **Usage: SeqSero2.py**
estrain@8 154
estrain@8 155 **Algorithms for BWA mapping**
estrain@8 156
estrain@8 157 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
estrain@8 158
estrain@8 159 ]]></help>
estrain@8 160 <citations>
estrain@8 161 <citation type="bibtex">
estrain@8 162 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
estrain@8 163 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
estrain@8 164 journal={J Clin Microbiol}, publisher={ASM},
estrain@8 165 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
estrain@8 166 year={2015}, month={Max},
estrain@8 167 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
estrain@8 168 }</citation>
estrain@8 169 <citation type="bibtex">
estrain@8 170 @misc{cfsan_biostatistics_group_2017,
estrain@8 171 title={CFSAN Biostatistics Group fork of SeqSero2},
estrain@8 172 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
estrain@8 173 </citation>
estrain@8 174 </citations>
estrain@8 175
estrain@8 176 </tool>