comparison integrate.xml @ 1:74fa68f4e579 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c

0:4341b8ff2a46

<tool id="seurat_integrate" name="Seurat Integrate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description> and manipulate layers </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@
    ]]></command>

@CMD_imports@
@CMD_read_inputs@

#if $method.method == 'SplitLayers'
    seurat_obj[['$method.assay']]<-split(
        seurat_obj[['$method.assay']], 
        f = seurat_obj[['$method.factor', drop = TRUE]]
    )

#else if $method.method == 'IntegrateLayers'

    #if $method.features
    features_list<-paste(readLines('$method.features'), collapse=",")
    #end if

    seurat_obj<-IntegrateLayers(
        seurat_obj, 
        method = $method.integration.integration_method,
        #if $method.integration.integration_method == 'CCAIntegration'
            #if $method.integration.adv.k_filter
            k.filter = $method.integration.adv.k_filter,
            #else           
            k.filter = NA,
            #end if
            dims = 1:$method.integration.adv.dims,
            #if $method.integration.adv.dims_to_integrate
            dims.to.integrate = $method.integration.adv.dims_to_integrate,

            sd.weight = $method.integration.adv.sd_weight,
            preserve.order = $method.integration.adv.preserve_order,
        #else if $method.integration.integration_method == 'RPCAIntegration'
            #if $method.integration.adv.k_filter
            k.filter = $method.integration.adv.k_filter,
            #else           
            k.filter = NA,
            #end if
            dims = 1:$method.integration.adv.dims,
            #if $method.integration.adv.dims_to_integrate
            dims.to.integrate = $method.integration.adv.dims_to_integrate,

            weight.reduction = c(unlist(strsplit(gsub(" ", "", '$method.integration.adv.weight_reduction'), ","))),
            #end if
            sd.weight = $method.integration.adv.sd_weight,
            preserve.order = $method.integration.adv.preserve_order,
        #end if
        orig.reduction = '$method.orig_reduction', 
        new.reduction = '$method.new_reduction',
        #if $method.assay != ''
        assay = '$method.assay',
        #end if
        #if $method.features

            <!-- test1:  SplitLayers -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
            <conditional name="method">
                <param name="method" value="SplitLayers"/>
                <param name="assay" value="RNA"/>
                <param name="factor" value="Group"/>                 
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">

                <param name="method" value="IntegrateLayers"/>
                <conditional name="integration">
                    <param name="integration_method" value="HarmonyIntegration"/>
                </conditional>
                <param name="orig_reduction" value="pca"/>
                <param name="new_reduction" value="integrated.harm"/>            
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">

    </tests>
    <help><![CDATA[
Seurat
======

Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 

Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.


Split

Integrate
=========

Multiple layers are integrated to enable them to be analysed together. 

Available methods are: CCA, Harmony, JointPCA, RPCA, FastMNN and scVI.

More details on the `seurat documentation
<https://satijalab.github.io/seurat-object/reference/CreateSeuratObject.html>`__

<https://satijalab.github.io/seurat-object/reference/SplitLayers.html>`__

PrepSCTFindMarkers
==================

Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate. 
The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/prepsctfindmarkers>`__

1:74fa68f4e579

<tool id="seurat_integrate" name="Seurat Integrate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description> and manipulate layers </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@
    ]]></command>

@CMD_imports@
@CMD_read_inputs@

#if $method.method == 'SplitLayers'
    seurat_obj[['$method.assay']]<-split(
        seurat_obj[['$method.assay']],
        f = seurat_obj[['$method.factor', drop = TRUE]]
    )

#else if $method.method == 'IntegrateLayers'

    #if $method.features
    features_list<-paste(readLines('$method.features'), collapse=",")
    #end if

    seurat_obj<-IntegrateLayers(
        seurat_obj,
        method = $method.integration.integration_method,
        #if $method.integration.integration_method == 'CCAIntegration'
            #if $method.integration.adv.k_filter
            k.filter = $method.integration.adv.k_filter,
            #else
            k.filter = NA,
            #end if
            dims = 1:$method.integration.adv.dims,
            #if $method.integration.adv.dims_to_integrate
            dims.to.integrate = $method.integration.adv.dims_to_integrate,

            sd.weight = $method.integration.adv.sd_weight,
            preserve.order = $method.integration.adv.preserve_order,
        #else if $method.integration.integration_method == 'RPCAIntegration'
            #if $method.integration.adv.k_filter
            k.filter = $method.integration.adv.k_filter,
            #else
            k.filter = NA,
            #end if
            dims = 1:$method.integration.adv.dims,
            #if $method.integration.adv.dims_to_integrate
            dims.to.integrate = $method.integration.adv.dims_to_integrate,

            weight.reduction = c(unlist(strsplit(gsub(" ", "", '$method.integration.adv.weight_reduction'), ","))),
            #end if
            sd.weight = $method.integration.adv.sd_weight,
            preserve.order = $method.integration.adv.preserve_order,
        #end if
        orig.reduction = '$method.orig_reduction',
        new.reduction = '$method.new_reduction',
        #if $method.assay != ''
        assay = '$method.assay',
        #end if
        #if $method.features

            <!-- test1:  SplitLayers -->
            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
            <conditional name="method">
                <param name="method" value="SplitLayers"/>
                <param name="assay" value="RNA"/>
                <param name="factor" value="Group"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">

                <param name="method" value="IntegrateLayers"/>
                <conditional name="integration">
                    <param name="integration_method" value="HarmonyIntegration"/>
                </conditional>
                <param name="orig_reduction" value="pca"/>
                <param name="new_reduction" value="integrated.harm"/>
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true"/>
            </section>
            <output name="hidden_output">

    </tests>
    <help><![CDATA[
Seurat
======

Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.

Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.


Split

Integrate
=========

Multiple layers are integrated to enable them to be analysed together.

Available methods are: CCA, Harmony, JointPCA, RPCA, FastMNN and scVI.

More details on the `seurat documentation
<https://satijalab.github.io/seurat-object/reference/CreateSeuratObject.html>`__

<https://satijalab.github.io/seurat-object/reference/SplitLayers.html>`__

PrepSCTFindMarkers
==================

Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate.
The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts.

More details on the `seurat documentation
<https://satijalab.org/seurat/reference/prepsctfindmarkers>`__