Skip to content

Metabolite Profile Datasets #78

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jbrestel wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Metabolite Profile Datasets #78

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 9 additions & 6 deletions Main/lib/xml/workflow/metaboliteProfiles.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,24 @@
<param name="experimentVersion"/>
<param name="gusConfigFile"/>

<constant name="dataDir">$$parentDataDir$$/$$experimentName$$</constant>
<constant name="workingDir">$$dataDir$$/workingDir</constant>
<constant name="resultsDir">$$dataDir$$/outputDir</constant>
<constant name="workingDir">$$parentDataDir$$/workingDir</constant>
<constant name="resultsDir">$$parentDataDir$$/outputDir</constant>

<step name="makeWorkingDir" stepClass="ReFlow::StepClasses::MakeDataDir">
<paramValue name="dataDir">$$workingDir$$</paramValue>
</step>

<step name="makeProfiles" stepClass="ApiCommonWorkflow::Main::WorkflowSteps::StudyAssayResultsNextflow">
<paramValue name="analysisConfigFile">$$experimentName$$/final/analysisConfig.xml</paramValue>
<paramValue name="finalDir">$$experimentName$$/final</paramValue>
<paramValue name="analysisConfigFile">$$parentDataDir$$/final/analysisConfig.xml</paramValue>
<paramValue name="finalDir">$$parentDataDir$$/final</paramValue>
<paramValue name="workingDir">$$workingDir$$</paramValue>
<paramValue name="resultsDir">$$resultsDir$$</paramValue>
<paramValue name="technologyType">metabolite_massSpec</paramValue>
<paramValue name="nextflowWorkflow">VEuPathDB/study-assay-results-nextflow</paramValue>
<paramValue name="isGitRepo">true</paramValue>
<depends name="makeWorkingDir"/>
</step>


<step name="loadStudyResultsFromConfig" stepClass="ApiCommonWorkflow::Main::WorkflowSteps::InsertStudyResults" stepLoadTypes="plugin">
<paramValue name="configFile">$$dataDir$$/outputDir/insert_study_results_config.txt</paramValue>
<paramValue name="inputDir">$$dataDir$$/outputDir</paramValue>
Expand Down
19 changes: 11 additions & 8 deletions Main/lib/xml/workflowTemplates/project.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -716,7 +716,12 @@
</subgraph>
</datasetTemplate>

<!-- old template deprecated-->
<step name="makeMetabolomicsDataDir" stepClass="ReFlow::StepClasses::MakeDataDir">
<paramValue name="dataDir">$$dataDir$$/metabolomics</paramValue>
<depends name="makeDataDir"/>
</step>

<!-- old template but still in use -->
<datasetTemplate class="metaboliteProfiles">
<prop name="experimentName"/>
<prop name="experimentVersion"/>
Expand All @@ -725,24 +730,22 @@
<paramValue name="gusConfigFile">$$projectGusConfigFile$$</paramValue>
<paramValue name="datasetName">metaboliteProfiles_${experimentName}_RSRC</paramValue>
<paramValue name="datasetLoaderXmlFileName">$$projectName$$.xml</paramValue>
<paramValue name="parentDataDir">$$dataDir$$</paramValue>
<paramValue name="parentDataDir">$$dataDir$$/metabolomics</paramValue>
<depends name="makeMetabolomicsDataDir"/>
<!--<dependsGlobal name="chEBI_Compounds"/>-->
</subgraph>

<subgraph name="MetaboliteProfiles" xmlFile="metaboliteProfiles.xml">
<paramValue name="gusConfigFile">$$projectGusConfigFile$$</paramValue>
<paramValue name="parentDataDir">$$dataDir$$</paramValue>
<paramValue name="parentDataDir">$$dataDir$$/metabolomics/metaboliteProfiles_${experimentName}_RSRC</paramValue>
<paramValue name="experimentName">metaboliteProfiles_${experimentName}_RSRC</paramValue>
<paramValue name="experimentVersion">${experimentVersion}</paramValue>
<depends name="metaboliteProfiles_${experimentName}_RSRC"/>
</subgraph>

</datasetTemplate>

<!-- new template for untargeted metabolomics -->
<step name="makeMetabolomicsDataDir" stepClass="ReFlow::StepClasses::MakeDataDir">
<paramValue name="dataDir">$$dataDir$$/metabolomics</paramValue>
<depends name="makeDataDir"/>
</step>
<!-- new template for untargeted metabolomics BUT not used on frontend yet -->

<datasetTemplate class="compoundMassSpec">
<prop name="experimentName"/>
Expand Down