Mercurial > repos > jpayne > seqsero_v2
changeset 15:1d6702e0bffd
Uploaded
| author | estrain |
|---|---|
| date | Wed, 01 Mar 2023 13:20:59 -0500 |
| parents | 496f5f2b5e75 |
| children | 3b6d5b60968f |
| files | seqsero.xml |
| diffstat | 1 files changed, 192 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqsero.xml Wed Mar 01 13:20:59 2023 -0500 @@ -0,0 +1,192 @@ +<tool id="seqsero_v2" name="SeqSero2 v1.2.1" version="8"> + <description>Salmonella serotype prediction</description> + <macros> + <token name="@VERSION@">1.2.1</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">seqsero2</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + echo "SeqSero2 v1.2.1"; + mkdir ./output; + + #if $reads.reads_select == 'history' + #set $name = $reads.forward.name.split('.')[0].replace(' ','_') + #set $forward = $reads.forward + #set $reverse = $reads.reverse + #set $infile = $name + "_1.fastq " + $name + "_2.fastq" + #set $tval = 2 + #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz') + gunzip -c $reverse > reverse.fastq; + #set $reverse = './reverse.fastq' + gunzip -c $forward > forward.fastq; + #set $forward = './forward.fastq' + #end if + ln -s $forward ${name}_1.fastq; + ln -s $reverse ${name}_2.fastq; + #else if $reads.reads_select == 'collection' + #set $name = $reads.coll.name.replace(' ', '_') + #set $forward = $reads.coll.forward + #set $reverse = $reads.coll.reverse + #set $infile = $name + "_1.fastq " + $name + "_2.fastq" + #set $tval = 2 + #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz') + gunzip -c $reverse > reverse.fastq; + #set $reverse = './reverse.fastq' + gunzip -c $forward > forward.fastq; + #set $forward = './forward.fastq' + #end if + ln -s $forward ${name}_1.fastq; + ln -s $reverse ${name}_2.fastq; + #else + #set $name = $reads.assembly.name.replace(' ', '_') + #set $ga = $reads.assembly + #set $infile = $name + ".fasta" + ln -s $ga ${name}.fasta; + #set $tval = 4 + #set $mode='k' + #end if + echo $name ; + echo "-=-=-=-=-" ; + touch output/SeqSero_log.txt ; + SeqSero2_package.py + -p \${GALAXY_SLOTS:-1} + -t $tval + -m $mode + -d ./output + #if $mode == 'a': + -b $maptype + #end if + -i $infile && + echo "-=-=-=-=-" && + cat output/SeqSero_log.txt && + echo "-=-=-=-=-" && + ls -lah ./output + ]]></command> + <inputs> + + <conditional name="reads"> + <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history"> + <option value="collection">Paired collection from your history</option> + <option value="history">Two FASTQ datasets from your history</option> + <option value="genome">Genome Assembly</option> + </param> + <when value="collection"> + <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" /> + </when> + <when value="history"> + <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> + <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> + </when> + <when value="genome"> + <param label="Genome assembly" name="assembly" type="data" format="fasta"/> + </when> + </conditional> + + <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" /> + <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> --> + <!-- <param name="numofthr" type="select" label="Number of threads"> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="4">4</option> --> + <!-- </param> --> + + <param label="Analysis mode" type="select" name="mode"> + <option value="a">allele mode</option> + <option value="k">k-mer mode</option> + </param> + + <param name="maptype" type="select" label="Algorithms for BWA mapping"> + <option value="mem">mem</option> + <option value="sam">sam</option> + </param> + + + + </inputs> + <outputs> + <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/> + </outputs> + <tests> + <!-- <test> + <param name="reads_select" value="history" /> + <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" /> + <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" /> + <output name="results" file="Seqsero_result.tsv" /> + </test> + <test> + <param name="reads_select" value="collection" /> + <param name="coll"> + <collection type="paired"> + <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" /> + </collection> + </param> + <output name="results" file="Seqsero_result.tsv" /> + </test> --> + <test> + <param name="mode" value="k" /> + <param name="reads_select" value="history" /> + <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" /> + <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" /> + <output name="results" file="Seqsero_result_25k.tsv" /> + </test> + <test> + <param name="mode" value="k" /> + <param name="reads_select" value="collection" /> + <param name="coll"> + <collection type="paired"> + <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> + </collection> + </param> + <output name="results" file="Seqsero_result_25k_coll.tsv" /> + </test> + <test> + <param name="mode" value="a" /> + <param name="reads_select" value="history" /> + <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" /> + <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" /> + <assert_stdout> + <has_text text="predicted antigenic profile does not exist" /> + </assert_stdout> + </test> + <!-- <test> + <param name="mode" value="a" /> + <param name="reads_select" value="collection" /> + <param name="coll"> + <collection type="paired"> + <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> + </collection> + </param> + <output name="results" file="Seqsero_result_allele.tsv" /> + </test> --> + </tests> + <help><![CDATA[ + +**Usage: SeqSero2.py** + +**Algorithms for BWA mapping** + +'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode + + ]]></help> + <citations> + <citation type="bibtex"> + @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015, + title={Salmonella serotype determination utilizing high-throughput genome sequencing data.}, + journal={J Clin Microbiol}, publisher={ASM}, + author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.}, + year={2015}, month={Max}, + url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}}, + }</citation> + <citation type="bibtex"> + @misc{cfsan_biostatistics_group_2017, + title={CFSAN Biostatistics Group fork of SeqSero2}, + url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}}, + </citation> + </citations> + +</tool>