# HG changeset patch # User jpayne # Date 1755287479 0 # Node ID 225680ef4cc1efa4352858258eba2eac83af3a4c planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty diff -r 000000000000 -r 225680ef4cc1 index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/index.html Fri Aug 15 19:51:19 2025 +0000 @@ -0,0 +1,284 @@ + + + + + + + + + + + + + + Quay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + \ No newline at end of file diff -r 000000000000 -r 225680ef4cc1 job_conf.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/job_conf.yml Fri Aug 15 19:51:19 2025 +0000 @@ -0,0 +1,34 @@ +runners: + local: + load: galaxy.jobs.runners.local:LocalJobRunner + workers: 16 + +# handling: +# processes: +# handler0: + +execution: + default: local + environments: + local: + runner: local + docker_local: + runner: local + docker_enabled: true + # container: "auto" + docker_volumes: $defaults + # docker_set_user: null + docker_run_extra_arguments: "--entrypoint ''" + docker_set_user: root + +tools: +- id: seqsero2 + # handler: handler0 + environment: docker_local + +limits: +- + # Amount of time a job can run (in any environment) before it + # will be terminated by Galaxy. + type: walltime + value: '01:00:00' \ No newline at end of file diff -r 000000000000 -r 225680ef4cc1 seqsero2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqsero2.xml Fri Aug 15 19:51:19 2025 +0000 @@ -0,0 +1,203 @@ + + Salmonella serotype prediction + + 1.3.1 + + + + + seqsero2:1.3.1 + + + 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 --version ; + echo "-=-=-=-=-" ; + 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 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @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}}, + } + + @misc{cfsan_biostatistics_group_2017, + title={CFSAN Biostatistics Group fork of SeqSero2}, + url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}}, + + + + diff -r 000000000000 -r 225680ef4cc1 seqsero2S.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqsero2S.xml Fri Aug 15 19:51:19 2025 +0000 @@ -0,0 +1,202 @@ + + Simplified Salmonella serotype prediction + + 1.1.3 + + + + + seqsero2s:1.1.3 + + + 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 ; + $__tool_directory__/SeqSero2_package.py --version ; + echo "-=-=-=-=-" ; + 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 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @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}}, + } + + @misc{cfsan_biostatistics_group_2017, + title={CFSAN Biostatistics Group fork of SeqSero2}, + url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}}, + + + + diff -r 000000000000 -r 225680ef4cc1 test-data/.gitmodules --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.gitmodules Fri Aug 15 19:51:19 2025 +0000 @@ -0,0 +1,3 @@ +[submodule "test/csp2"] + path = test/csp2 + url = https://github.com/CFSAN-Biostatistics/CSP2_TestData.git diff -r 000000000000 -r 225680ef4cc1 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Fri Aug 15 19:51:19 2025 +0000 @@ -0,0 +1,10 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +#test1 test1 Test-Genome ./test-data/test1.fa \ No newline at end of file