| Next changeset 1:46d49cf8db7d (2026-01-21) |
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Commit message:
planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty |
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added:
job_conf.yml seqsero2S.xml test-data/.gitmodules tool-data/all_fasta.loc.sample |
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| diff -r 000000000000 -r a9790ce778af job_conf.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/job_conf.yml Mon Sep 29 20:04:28 2025 +0000 |
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| @@ -0,0 +1,37 @@ +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: seqsero_v2 + # handler: handler0 + environment: docker_local +- id: seqsero2s + # 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 |
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| diff -r 000000000000 -r a9790ce778af seqsero2S.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqsero2S.xml Mon Sep 29 20:04:28 2025 +0000 |
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| b'@@ -0,0 +1,197 @@\n+<tool id="seqsero2s" name="SeqSero2S" version="1">\r\n+ <description>Simplified Salmonella serotype prediction</description>\r\n+ <requirements>\r\n+ <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> -->\r\n+ <container type="docker">quay.io/biocontainers/seqsero2s:1.1.3--pyhdfd78af_0</container>\r\n+ </requirements>\r\n+ <command detect_errors="exit_code"><![CDATA[\r\n+ mkdir ./output;\r\n+\r\n+ #if $reads.reads_select == \'history\'\r\n+ #set $name = $reads.forward.name.split(\'.\')[0].replace(\' \',\'_\')\r\n+ #set $forward = $reads.forward\r\n+ #set $reverse = $reads.reverse\r\n+ #set $infile = $name + "_1.fastq " + $name + "_2.fastq" \r\n+ #set $tval = 2\r\n+ #if $reverse.is_of_type(\'fastq.gz\', \'fastqsanger.gz\')\r\n+ gunzip -c $reverse > reverse.fastq;\r\n+ #set $reverse = \'./reverse.fastq\'\r\n+ gunzip -c $forward > forward.fastq;\r\n+ #set $forward = \'./forward.fastq\'\r\n+ #end if\r\n+ ln -s $forward ${name}_1.fastq;\r\n+ ln -s $reverse ${name}_2.fastq;\r\n+ #else if $reads.reads_select == \'collection\'\r\n+ #set $name = $reads.coll.name.replace(\' \', \'_\')\r\n+ #set $forward = $reads.coll.forward\r\n+ #set $reverse = $reads.coll.reverse\r\n+ #set $infile = $name + "_1.fastq " + $name + "_2.fastq" \r\n+ #set $tval = 2\r\n+ #if $reverse.is_of_type(\'fastq.gz\', \'fastqsanger.gz\')\r\n+ gunzip -c $reverse > reverse.fastq;\r\n+ #set $reverse = \'./reverse.fastq\'\r\n+ gunzip -c $forward > forward.fastq;\r\n+ #set $forward = \'./forward.fastq\'\r\n+ #end if\r\n+ ln -s $forward ${name}_1.fastq;\r\n+ ln -s $reverse ${name}_2.fastq;\r\n+ #else \r\n+ #set $name = $reads.assembly.name.replace(\' \', \'_\')\r\n+ #set $ga = $reads.assembly\r\n+ #set $infile = $name + ".fasta" \r\n+ ln -s $ga ${name}.fasta;\r\n+ #set $tval = 4\r\n+ #set $mode=\'k\'\r\n+ #end if\r\n+ echo $name ;\r\n+ echo "-=-=-=-=-" ;\r\n+ touch output/SeqSero_log.txt ;\r\n+ /usr/local/bin/SeqSero2S.py --version ;\r\n+ echo "-=-=-=-=-" ;\r\n+ /usr/local/bin/SeqSero2S.py\r\n+ -p \\${GALAXY_SLOTS:-1}\r\n+ -t $tval \r\n+ -m $mode\r\n+ -d ./output\r\n+ #if $mode == \'a\':\r\n+ -b $maptype \r\n+ #end if\r\n+ -i $infile &&\r\n+ echo "-=-=-=-=-" &&\r\n+ cat output/SeqSero_log.txt &&\r\n+ echo "-=-=-=-=-" &&\r\n+ ls -lah ./output\r\n+ ]]></command>\r\n+ <inputs>\r\n+ \r\n+ <conditional name="reads">\r\n+ <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">\r\n+ <option value="collection">Paired collection from your history</option>\r\n+ <option value="history">Two FASTQ datasets from your history</option>\r\n+ <option value="genome">Genome Assembly</option>\r\n+ </param>\r\n+ <when value="collection">\r\n+ <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />\r\n+ </when>\r\n+ <when value="history">\r\n+ <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />\r\n+ <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />\r\n+ </when>\r\n+ <when value="genome">\r\n+ <param label="Genome assembly" name="assembly" type="data" format="fasta"/>\r\n+ </when>\r\n+ </conditional>\r\n+ \r\n+ <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />\r\n+ <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->\r\n+ <!-- <param name="numofthr" type="select" label="Number of '..b'ds_select" value="history" />\r\n+ <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />\r\n+ <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />\r\n+ <output name="results" file="Seqsero_result.tsv" />\r\n+ </test>\r\n+ <test>\r\n+ <param name="reads_select" value="collection" />\r\n+ <param name="coll">\r\n+ <collection type="paired">\r\n+ <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />\r\n+ <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />\r\n+ </collection>\r\n+ </param>\r\n+ <output name="results" file="Seqsero_result.tsv" />\r\n+ </test> -->\r\n+ <!-- <test>\r\n+ <param name="mode" value="k" />\r\n+ <param name="reads_select" value="history" />\r\n+ <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />\r\n+ <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />\r\n+ <output name="results" file="Seqsero_result_25k.tsv" />\r\n+ </test>\r\n+ <test>\r\n+ <param name="mode" value="k" />\r\n+ <param name="reads_select" value="collection" />\r\n+ <param name="coll">\r\n+ <collection type="paired">\r\n+ <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />\r\n+ <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />\r\n+ </collection>\r\n+ </param>\r\n+ <output name="results" file="Seqsero_result_25k_coll.tsv" />\r\n+ </test>\r\n+ <test>\r\n+ <param name="mode" value="a" />\r\n+ <param name="reads_select" value="history" />\r\n+ <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />\r\n+ <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />\r\n+ <assert_stdout>\r\n+ <has_text text="input genome cannot be identified as Salmonella" />\r\n+ </assert_stdout>\r\n+ </test> -->\r\n+ <!-- <test>\r\n+ <param name="mode" value="a" />\r\n+ <param name="reads_select" value="collection" />\r\n+ <param name="coll">\r\n+ <collection type="paired">\r\n+ <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />\r\n+ <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />\r\n+ </collection>\r\n+ </param>\r\n+ <output name="results" file="Seqsero_result_allele.tsv" />\r\n+ </test> -->\r\n+ <test>\r\n+ <param name="mode" value="k" />\r\n+ <param name="reads_select" value="genome" />\r\n+ <param name="assembly" value="test/taxonomy/salmonella/contigs.fa" ftype="fasta" />\r\n+ <output name="results" file="test/taxonomy/salmonella/SeqSero_result/SeqSero_result.tsv" />\r\n+ </test>\r\n+ </tests>\r\n+ <help><![CDATA[\r\n+ \r\n+**Usage: SeqSero2.py** \r\n+\r\n+**Algorithms for BWA mapping**\r\n+\r\n+\'mem\' for mem, \'sam\' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode\r\n+ \r\n+ ]]></help>\r\n+ <citations>\r\n+ <citation type="bibtex">\r\n+ @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,\r\n+ title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},\r\n+ journal={J Clin Microbiol}, publisher={ASM},\r\n+ author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},\r\n+ year={2015}, month={Max},\r\n+ url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},\r\n+ }</citation>\r\n+ <citation type="bibtex">\r\n+ @misc{cfsan_biostatistics_group_2017,\r\n+ title={CFSAN Biostatistics Group fork of SeqSero2},\r\n+ url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},\r\n+ </citation>\r\n+ </citations>\r\n+\r\n+</tool>\r\n' |
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| diff -r 000000000000 -r a9790ce778af test-data/.gitmodules --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.gitmodules Mon Sep 29 20:04:28 2025 +0000 |
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| @@ -0,0 +1,3 @@ +[submodule "test/csp2"] + path = test/csp2 + url = https://github.com/CFSAN-Biostatistics/CSP2_TestData.git |
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| diff -r 000000000000 -r a9790ce778af tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Mon Sep 29 20:04:28 2025 +0000 |
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| @@ -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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +#test1 test1 Test-Genome ./test-data/test1.fa \ No newline at end of file |