Mercurial > repos > jpayne > seqsero_v2
changeset 14:496f5f2b5e75
Uploaded
| author | estrain |
|---|---|
| date | Tue, 14 Feb 2023 12:11:27 -0500 |
| parents | 3513b93ebe6a |
| children | 1d6702e0bffd |
| files | seqsero2.xml |
| diffstat | 1 files changed, 57 insertions(+), 39 deletions(-) [+] |
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--- a/seqsero2.xml Tue Sep 03 12:40:46 2019 -0400 +++ b/seqsero2.xml Tue Feb 14 12:11:27 2023 -0500 @@ -1,49 +1,63 @@ -<tool id="seqsero_v2" name="SeqSero 2" version="2.0.1"> +<tool id="seqsero2v111" 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="3.6">python</requirement> - <requirement type="package" version="1.70">biopython</requirement> - <requirement type="package" version="2.7.1">blast</requirement> - <requirement type="package" version="1.9">samtools</requirement> - <requirement type="package" version="2.9.1">sra-tools</requirement> - <requirement type="package" version="0.7.17">bwa</requirement> - <requirement type="package" version="3.13.1">spades</requirement> - <requirement type="package" version="2.27.1">bedtools</requirement> + <requirement type="package" version="@VERSION@">seqsero2</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - echo "SeqSero 2 v. 1.0.0" ; + 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 - #else - #set $name = $reads.coll.name.replace(' ', '_') - #set $forward = $reads.coll.forward - #set $reverse = $reads.coll.reverse - #end if - echo $name ; - echo "-=-=-=-=-" ; - #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz') - gunzip -c $forward > forward.fastq; - #set $forward = './forward.fastq' - #end if - #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz') - gunzip -c $reverse > reverse.fastq; - #set $reverse = './reverse.fastq' - #end if + #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; - mkdir ./output; - touch output/SeqSero_log.txt ; - python $__tool_directory__/SeqSero2/SeqSero2_package.py - -p \${GALAXY_SLOTS:-4} - -t 2 + #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 ${name}_1.fastq ${name}_2.fastq && + -i $infile && echo "-=-=-=-=-" && cat output/SeqSero_log.txt && echo "-=-=-=-=-" && @@ -52,9 +66,10 @@ <inputs> <conditional name="reads"> - <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> + <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" /> @@ -63,6 +78,9 @@ <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" /> @@ -75,8 +93,8 @@ <!-- </param> --> <param label="Analysis mode" type="select" name="mode"> - <option value="a">allele mode</option> - <option value="k">k-mer mode</option> + <option value="a">allele mode</option> + <option value="k">k-mer mode</option> </param> <param name="maptype" type="select" label="Algorithms for BWA mapping"> @@ -88,7 +106,7 @@ </inputs> <outputs> - <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/> + <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/> </outputs> <tests> <!-- <test> @@ -131,7 +149,7 @@ <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" /> + <has_text text="predicted antigenic profile does not exist" /> </assert_stdout> </test> <!-- <test>