Mercurial > repos > jpayne > seqsero2
changeset 0:225680ef4cc1 draft
planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty
| author | jpayne |
|---|---|
| date | Fri, 15 Aug 2025 19:51:19 +0000 |
| parents | |
| children | b747b2c8fdb6 |
| files | index.html job_conf.yml seqsero2.xml seqsero2S.xml test-data/.gitmodules tool-data/all_fasta.loc.sample |
| diffstat | 6 files changed, 736 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<!DOCTYPE html> +<html ng-app="quay" class="hosted"> + <head> + + + + <script id="trustarc" src="//static.redhat.com/libs/redhat/marketing/latest/trustarc/trustarc.js"></script> + <script id="dpal" src="https://www.redhat.com/ma/dpal.js" type="text/javascript"></script> + + + <base href="/"> + + + <title ng-bind="title + ' ยท Quay'">Quay</title> + + + + <base href="/"> + + <meta id="descriptionTag" name="description" content="Quay is the best place to build, store, and distribute your containers. Public repositories are always free." /> + <meta name="google-site-verification" content="GalDznToijTsHYmLjJvE4QaB9uk_IP16aaGDz5D75T4" /> + <meta name="google-site-verification" content="oio7ioMILUo9QDflvyFz8pWig1ac2eLq5IGyQuzFMh8" /> + + + + + + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + + + <link rel="stylesheet" href="/static/ldn/font-awesome.css-a166e3c966c6.css" type="text/css"> + + <link rel="stylesheet" href="/static/ldn/bootstrap.min.css-13f668494557.css" type="text/css"> + + <link rel="stylesheet" href="/static/ldn/cssfamilySourceSansPro300400700-30cd793a4b9b.css" type="text/css"> + + <link rel="stylesheet" href="/static/ldn/bootstrap-datetimepicker.min.css-4b15a4ede750.css" type="text/css"> + + <link rel="stylesheet" href="/static/ldn/cal-heatmap.css-904c3b9e8a60.css" type="text/css"> + + <link rel="stylesheet" href="/static/ldn/ng-tags-input.min.css-7782190f81cd.css" type="text/css"> + + + <!-- Icons --> + <link rel="shortcut icon" 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"getRepoBuildLogs", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "build_uuid", "required": true, "type": "string"}]}, "parameters": [{"in": "path", "name": "build_uuid", "required": true, "type": "string"}, {"in": "path", "name": "repository", "required": true, "type": "string"}], "x-name": "endpoints.api.build.RepositoryBuildLogs", "x-path": "/api/v1/repository/{repository}/build/{build_uuid}/logs", "x-tag": "build"}, "/api/v1/repository/{repository}/build/{build_uuid}/status": {"get": {"operationId": "getRepoBuildStatus", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "build_uuid", "required": true, "type": "string"}]}, "parameters": [{"in": "path", "name": "build_uuid", "required": true, "type": "string"}, {"in": "path", "name": "repository", "required": true, "type": "string"}], "x-name": "endpoints.api.build.RepositoryBuildStatus", "x-path": 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{"operationId": "getRepoManifest", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "manifestref", "required": true, "type": "string"}, {"in": "query", "name": "include_modelcard", "required": false, "type": "boolean"}]}, "parameters": [{"in": "path", "name": "manifestref", "required": true, "type": "string"}, {"in": "path", "name": "repository", "required": true, "type": "string"}], "x-name": "endpoints.api.manifest.RepositoryManifest", "x-path": "/api/v1/repository/{repository}/manifest/{manifestref}", "x-tag": "manifest"}, "/api/v1/repository/{repository}/manifest/{manifestref}/labels": {"get": {"operationId": "listManifestLabels", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "manifestref", "required": true, "type": "string"}, {"in": "query", "name": "filter", "required": false, "type": "string"}]}, "parameters": [{"in": "path", "name": "manifestref", "required": true, "type": "string"}, {"in": "path", "name": "repository", "required": true, "type": "string"}], "post": {"operationId": "addManifestLabel", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "manifestref", "required": true, "type": "string"}]}, "x-name": "endpoints.api.manifest.RepositoryManifestLabels", "x-path": "/api/v1/repository/{repository}/manifest/{manifestref}/labels", "x-tag": "manifest"}, "/api/v1/repository/{repository}/manifest/{manifestref}/labels/{labelid}": {"delete": {"operationId": "deleteManifestLabel", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "labelid", "required": true, "type": "string"}, {"in": "path", "name": "manifestref", "required": true, "type": "string"}]}, "get": {"operationId": "getManifestLabel", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": 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"path", "name": "repository", "required": true, "type": "string"}], "post": {"operationId": "testRepoNotification", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "uuid", "required": true, "type": "string"}]}, "x-name": "endpoints.api.repositorynotification.TestRepositoryNotification", "x-path": "/api/v1/repository/{repository}/notification/{uuid}/test", "x-tag": "repositorynotification"}, "/api/v1/repository/{repository}/permissions/team/": {"get": {"operationId": "listRepoTeamPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}]}, "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}], "x-name": "endpoints.api.permission.RepositoryTeamPermissionList", "x-path": "/api/v1/repository/{repository}/permissions/team/", "x-tag": "permission"}, "/api/v1/repository/{repository}/permissions/team/{teamname}": {"delete": {"operationId": "deleteTeamPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "teamname", "required": true, "type": "string"}]}, "get": {"operationId": "getTeamPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "teamname", "required": true, "type": "string"}]}, "parameters": [{"in": "path", "name": "teamname", "required": true, "type": "string"}, {"in": "path", "name": "repository", "required": true, "type": "string"}], "put": {"operationId": "changeTeamPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "teamname", "required": true, "type": "string"}]}, "x-name": "endpoints.api.permission.RepositoryTeamPermission", "x-path": "/api/v1/repository/{repository}/permissions/team/{teamname}", "x-tag": "permission"}, "/api/v1/repository/{repository}/permissions/user/": {"get": {"operationId": "listRepoUserPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}]}, "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}], "x-name": "endpoints.api.permission.RepositoryUserPermissionList", "x-path": "/api/v1/repository/{repository}/permissions/user/", "x-tag": "permission"}, "/api/v1/repository/{repository}/permissions/user/{username}": {"delete": {"operationId": "deleteUserPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "username", "required": true, "type": "string"}]}, "get": {"operationId": "getUserPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "username", "required": true, "type": "string"}]}, "parameters": [{"in": "path", "name": "username", "required": true, "type": "string"}, {"in": "path", "name": "repository", "required": true, "type": "string"}], "put": {"operationId": "changeUserPermissions", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "username", "required": true, "type": "string"}]}, "x-name": "endpoints.api.permission.RepositoryUserPermission", "x-path": "/api/v1/repository/{repository}/permissions/user/{username}", "x-tag": "permission"}, "/api/v1/repository/{repository}/permissions/user/{username}/transitive": {"get": {"operationId": "getUserTransitivePermission", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "path", "name": "username", "required": true, "type": "string"}]}, "parameters": [{"in": "path", "name": "username", "required": true, "type": "string"}, {"in": "path", "name": "repository", "required": true, "type": "string"}], "x-name": "endpoints.api.permission.RepositoryUserTransitivePermission", "x-path": "/api/v1/repository/{repository}/permissions/user/{username}/transitive", "x-tag": "permission"}, "/api/v1/repository/{repository}/tag/": {"get": {"operationId": "listRepoTags", "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}, {"in": "query", "name": "onlyActiveTags", "required": false, "type": "boolean"}, {"in": "query", "name": "page", "required": false, "type": "integer"}, {"in": "query", "name": "limit", "required": false, "type": "integer"}, {"in": "query", "name": "filter_tag_name", "required": false, "type": "string"}, {"in": "query", "name": "specificTag", "required": false, "type": "string"}]}, "parameters": [{"in": "path", "name": "repository", "required": true, "type": "string"}], "x-name": "endpoints.api.tag.ListRepositoryTags", "x-path": "/api/v1/repository/{repository}/tag/", "x-tag": "tag"}, "/api/v1/repository/{repository}/tag/{tag}": {"delete": {"operationId": "deleteFullTag", "parameters": [{"in": "path", "name": "repository", 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--- /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
--- /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 @@ +<tool id="seqsero_v2" name="SeqSero2 v1.3.1" version="9"> + <description>Salmonella serotype prediction</description> + <macros> + <token name="@VERSION@">1.3.1</token> + </macros> + <requirements> + <!-- <requirement type="package" version="@VERSION@">seqsero2</requirement> --> + <container> + <image>seqsero2:1.3.1</image> + </container> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + 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 --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 + ]]></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="input genome cannot be identified as Salmonella" /> + </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> --> + <test> + <param name="mode" value="a" /> + <param name="maptype" value="mem" /> + <param name="reads_select" value="genome" /> + <param name="assembly" value="test/taxonomy/salmonella/contigs.fa" ftype="fasta" /> + <output name="results" file="test/taxonomy/salmonella/SeqSero_result/Seqsero_result.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>
--- /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 @@ +<tool id="seqsero2s" name="SeqSero2S" version="1.1.3"> + <description>Simplified Salmonella serotype prediction</description> + <macros> + <token name="@VERSION@">1.1.3</token> + </macros> + <requirements> + <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> --> + <container> + <image>seqsero2s:1.1.3</image> + </container> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + 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 ; + $__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 + ]]></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="input genome cannot be identified as Salmonella" /> + </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> --> + <test> + <param name="mode" value="k" /> + <param name="reads_select" value="genome" /> + <param name="assembly" value="test/taxonomy/salmonella/contigs.fa" ftype="fasta" /> + <output name="results" file="test/taxonomy/salmonella/SeqSero_result/SeqSero_result.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>
--- /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
--- /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): +# +#<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