Mercurial > repos > lain > xseekerpreparator
diff XSeekerPreparator.xml @ 20:ce94e7a141bb draft default tip
" master branch Updating"
| author | lain |
|---|---|
| date | Tue, 06 Dec 2022 10:18:10 +0000 |
| parents | 2937e72e5891 |
| children |
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--- a/XSeekerPreparator.xml Tue Oct 18 12:57:28 2022 +0000 +++ b/XSeekerPreparator.xml Tue Dec 06 10:18:10 2022 +0000 @@ -1,34 +1,26 @@ -<tool id="xseeker_preparator" name="XSeeker Preparator" version="1.3.0"> +<tool id="xseeker_preparator" name="XSeeker Preparator" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> <description>prepares RData file from XCMS+CAMERA for XSeeker</description> + <macros> + <token name="@VERSION@">1.3.1</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <edam_operations> <edam_operation>operation_1812</edam_operation> <edam_operation>operation_0335</edam_operation> </edam_operations> <requirements> - <requirement type="package" >bioconductor-xcms</requirement> - <requirement type="package" version="1.48.0">bioconductor-camera</requirement> - <requirement type="package" >git</requirement> - <requirement type="package" >r-blob</requirement> - <requirement type="package" >r-dbi</requirement> - <requirement type="package" >r-fst</requirement> - <requirement type="package" >r-optparse</requirement> - <requirement type="package" >r-stringr</requirement> - <requirement type="package" >r-purrr</requirement> - <requirement type="package" >r-rsqlite</requirement> - <requirement type="package" >r-dbmodelr</requirement> - <!-- - <requirement type="package" version="3.12.0">bioconductor-xcms</requirement> + <requirement type="package" version="4.1.3">r-base</requirement> + <requirement type="package" version="3.14.0">bioconductor-xcms</requirement> <requirement type="package" version="1.48.0">bioconductor-camera</requirement> <requirement type="package" version="2.29.2">git</requirement> - <requirement type="package" version="1.2.1">r-blob</requirement> - <requirement type="package" version="1.1.0">r-dbi</requirement> - <requirement type="package" version="0.9.4">r-fst</requirement> + <requirement type="package" version="1.2.3">r-blob</requirement> + <requirement type="package" version="1.1.3">r-dbi</requirement> + <requirement type="package" version="0.9.8">r-fst</requirement> <requirement type="package" version="1.6.6">r-optparse</requirement> <requirement type="package" version="1.4.0">r-stringr</requirement> - <requirement type="package" version="0.3.4">r-purrr</requirement> - <requirement type="package" version="2.2.1">r-rsqlite</requirement> + <requirement type="package" version="0.3.5">r-purrr</requirement> + <requirement type="package" version="2.2.18">r-rsqlite</requirement> <requirement type="package" version="0.2.0">r-dbmodelr</requirement> - --> </requirements> <stdio> <exit_code @@ -67,104 +59,14 @@ #else --models '${database.models.url}' #end if - #if $class_column - --class '${class_column}' + #if $class + --class '${class}' #end if ]]> </command> - <inputs> - <param - name="input" - type="data" - multiple="false" - label="Rdata to prepare" - optional="false" - format="rdata" - > - </param> - <param - name="class_column" - type="text" - value="" - label="Column class name" - help=" - The name of the column containing the classes - - leave empty to let xsprep guess - " - optional="true" - > - </param> - <section name="samples" title="Samples Options" expanded="false"> - <param - name="selected" - type="data" - multiple="true" - label="Samples to visualize" - optional="true" - format="mzml" - > - </param> - </section> - <section name="database" title="Database Options" expanded="false"> - <param - name="archetypes" - type="select" - multiple="true" - label="Molecule family (for database's compounds enrichment)" - > - <option value="G" selected="true">General</option> - <option value="H">Halogenates</option> - </param> - <conditional name="base"> - <param name="kind" type="select" label="File containing compound's type"> - <option value="none" selected="true">None (deafult)</option> - <option value="tabular">tabular</option> - <option value="sql">sql</option> - </param> - <when value="tabular"> - <param - name="tabular" - type="data" - multiple="true" - label="Tabular file containing compound to use in XSeeker" - optional="true" - format="tabular" - > - </param> - </when> - <when value="sql"> - <param - name="sql" - type="data" - multiple="true" - label="SQL file containing compound to use in XSeeker" - optional="true" - format="sql" - > - </param> - </when> - </conditional> - <conditional name="models"> - <param name="kind" type="select" label="How is the database's model defined"> - <option value="default" selected="true">Default (regular XSeeker Database)</option> - <option value="url">Download model file</option> - <option value="git">Get versionned model file</option> - </param> - <when value="url"> - <param name="url" type="text" format="url" label="File URL"/> - </when> - <when value="git"> - <param name="url" type="text" format="url" label="Repo URL"/> - </when> - </conditional> - </section> - </inputs> - <outputs> - <data format="sqlite" name="output" /> - <!-- <data format="xseeker.sqlite" name="output" /> --> - </outputs> <configfiles> <configfile name="base_config"> +<![CDATA[ tryCatch({ DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER")) }, error=function(e) { @@ -340,6 +242,179 @@ ) ) ) + ]]> </configfile> </configfiles> + <inputs> + <param + argument="input" + type="data" + multiple="false" + optional="false" + format="rdata" + label="Rdata to prepare" + help=" + This rdata must be produced by a xcms+camera processing + and original files must still be in the history. + " + > + </param> + <param + argument="class" + type="text" + value="" + label="Column class name" + help=" + The name of the column containing the classes - + leave empty to let XSeeker Preparator guess + " + optional="true" + > + </param> + <section name="samples" title="Samples Options" expanded="false"> + <param + name="selected" + type="data" + multiple="true" + label="Samples to visualize" + optional="true" + format="mzml" + > + </param> + </section> + <section name="database" title="Database Options" expanded="false"> + <param + name="archetypes" + type="select" + multiple="true" + label="Molecule family (for database's compounds enrichment)" + > + <option value="G" selected="true">General</option> + <option value="H">Halogenates</option> + </param> + <conditional name="base"> + <param name="kind" type="select" label="File containing compound's type"> + <option value="none" selected="true">None (default)</option> + <option value="tabular">tabular</option> + <option value="sql">sql</option> + </param> + <when value="none" /> + <when value="sql" /> + <when value="tabular"> + <param + name="tabular" + type="data" + multiple="true" + label="Tabular file containing compound to use in XSeeker" + optional="true" + format="tabular" + > + </param> + </when> + <when value="sql"> + <param + name="sql" + type="data" + multiple="true" + label="SQL file containing compound to use in XSeeker" + optional="true" + format="sql" + > + </param> + </when> + </conditional> + <conditional name="models"> + <param name="kind" type="select" label="How is the database's model defined"> + <option value="default" selected="true">Default (regular XSeeker Database)</option> + <option value="url">Download model file</option> + <option value="git">Get versionned model file</option> + </param> + <when value="default" /> + <when value="url"> + <param name="url" type="text" format="url" label="File URL"/> + </when> + <when value="git"> + <param name="url" type="text" format="url" label="Repo URL"/> + </when> + </conditional> + </section> + </inputs> + <outputs> + <data format="sqlite" name="output" /> + <!-- <data format="xseeker.sqlite" name="output" /> --> + </outputs> + <help> + +.. class:: infomark + +**Authors** Lain Pavot (lain.pavot@inrae.fr) + +-------------------------------------- + +================== +XSeeker Preparator +================== + +----------- +Description +----------- + +A preparation tool to precalculate and reorginize data from XCMS+CAMERA for +XSeeker displayer tool to display them faster (from 30 min/some hours to some seconds). + + +----------------- +Workflow position +----------------- + +**Upstream tools** + +================ ======================== =========== =============== + Name output file format parameter +================ ======================== =========== =============== + CAMERA rdata.camera.quick rdata +================ ======================== =========== =============== + + +**Downstream tools** + +================ ======================== =========== =============== + Name output file format parameter +================ ======================== =========== =============== + XSeeker sqlite sqlite3 NA +================ ======================== =========== =============== + + + +----------- +Input files +----------- + +Takes a rdata outputed by camera (after xcms) as input. The rdata has must have +been produced using some mzml files - mxml files which must still be present +in the history when doing xseekerpreparator: +The rdata contains only some data and the paths to the original mzml files. +These mzml files contains a lot of usefull informations needed to prepare +the data for XSeeker. These files are not given as input, but are still +needed. + +---------- +Parameters +---------- +Column class name: + - the name of the column that defines classes in your sample metadata. +Sample options: + - provide mzml file names to process. Other files defined in the rdata will + not be processed, and will not be available in xseeker. +Database Options: + - provide the molecular family you want to annotate, a compound file. + - The database's model can be re-defined - only for devs users. + +------------ +Output files +------------ +An SQLite3 file is a database file that organizes data in such a way it is +easily stored, filtered, modified, retrieved. + </help> + <citations></citations> </tool>