seurat_scale_data: seurat_macros.xml comparison

comparison seurat_macros.xml @ 6:5e9ba303f9e1 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6

author	ebi-gxa
date	Sat, 02 Mar 2024 10:42:19 +0000
parents	d2f6eac0ad42
children

comparison

equal deleted inserted replaced

-:d2f6eac0ad42
+:5e9ba303f9e1
 <?xml version="1.0"?>
 <macros>
-<token name="@VERSION@">0.3.0</token>
+<token name="@VERSION@">4.0.0</token>
-<token name="@SEURAT_VERSION@">3.2.3</token>
+<token name="@SEURAT_VERSION@">4.0.4</token>
 <xml name="requirements">
 <requirements>
 <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
 </requirements>
 </xml>
 	<version_command><![CDATA[
 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
 ]]></version_command>
 </xml>
-<xml name="input_object_params">
+<xml name="input_object_params" token_multiple="False" token_varname="input" token_optional="False">
-<conditional name="input" label="Input format">
+<conditional name="@VARNAME@" label="Input format">
-<param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData">
+<param type="select" name="format" label="Choose the format of the @VARNAME@" help="Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData">
 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
 <option value="loom">Loom</option>
+<option value="h5seurat">Seurat HDF5</option>
 <option value="anndata">AnnData</option>
 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
 </param>
 <when value="anndata">
-<param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/>
+<param type="data" name="anndata_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="AnnData file" help="Select AnnData files for @VARNAME@" format="h5,h5ad"/>
 </when>
 <when value="loom">
-<param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/>
+<param type="data" name="loom_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Loom file" help="Select Loom file(s) for @VARNAME@" format="h5,h5loom"/>
 </when>
 <when value="rds_seurat">
-<param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/>
+<param type="data" name="rds_seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Seurat object for @VARNAME@" format="rdata"/>
 </when>
 <when value="rds_sce">
-<param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/>
+<param type="data" name="rds_sce_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Single Cell Experiment object for @VARNAME@" format="rdata"/>
+</when>
+<when value="h5seurat">
+<param type="data" name="h5seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Seurat HDF5" help="Select Seurat HDF5 file(s) for @VARNAME" format="h5"/>
 </when>
 </conditional>
 </xml>
+<token name="@INPUT_OBJ_PREAMBLE@">
+#if $input.format == 'loom'
+ln -s '$input.loom_file' input.loom;
+#else if $input.format == 'h5seurat'
+ln -s '$input.h5seurat_file' input.h5seurat;
+#else if $input.format == 'anndata'
+## it complains when using links for AnnData...
+cp '$input.anndata_file' input.h5ad;
+#end if
+</token>
 <token name="@INPUT_OBJECT@">
 #if $input.format == "anndata"
---input-object-file '$input.anndata_file' --input-format anndata
+--input-object-file input.h5ad --input-format anndata
 #else if $input.format == "loom"
---input-object-file '$input.loom_file' --input-format loom
+--input-object-file input.loom --input-format loom
 #else if $input.format == "rds_seurat"
 --input-object-file '$input.rds_seurat_file' --input-format seurat
 #else if $input.format == "rds_sce"
 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
+#else if $input.format == "h5seurat"
+--input-object-file input.h5seurat --input-format h5seurat
+#end if
+</token>
+<token name="@QUERY_OBJ_PREAMBLE@">
+#if $query.format == 'loom'
+ln -s '$query.loom_file' query.loom;
+#else if $query.format == 'h5seurat'
+ln -s '$query.h5seurat_file' query.h5seurat;
+#else if $query.format == 'anndata'
+## it complains when using links for AnnData...
+cp '$query.anndata_file' query.h5ad;
+#end if
+</token>
+<token name="@QUERY_OBJECT@">
+#if $query.format == "anndata"
+--query-object-file query.h5ad --query-format anndata
+#else if $query.format == "loom"
+--query-object-file query.loom --query-format loom
+#else if $query.format == "rds_seurat"
+--query-object-file '$query.rds_seurat_file' --query-format seurat
+#else if $query.format == "rds_sce"
+--query-object-file '$query.rds_sce_file' --query-format singlecellexperiment
+#else if $query.format == "h5seurat"
+--query-object-file query.h5seurat --query-format h5seurat
+#end if
+</token>
+<token name="@ANCHORS_OBJ_PREAMBLE@">
+#if $anchors.format == 'loom'
+ln -s '$anchors.loom_file' anchors.loom;
+#else if $anchors.format == 'h5seurat'
+ln -s '$anchors.h5seurat_file' anchors.h5seurat;
+#else if $anchors.format == 'anndata'
+## it complains when using links for AnnData...
+cp '$anchors.anndata_file' anchors.h5ad;
+#end if
+</token>
+<token name="@ANCHORS_OBJECT@">
+#if $anchors.format == "anndata"
+--anchors-object-file anchors.h5ad --anchors-format anndata
+#else if $anchors.format == "loom"
+--anchors-object-file anchors.loom --anchors-format loom
+#else if $anchors.format == "rds_seurat"
+--anchors-object-file '$anchors.rds_seurat_file' --anchors-format seurat
+#else if $anchors.format == "rds_sce"
+--anchors-object-file '$anchors.rds_sce_file' --anchors-format singlecellexperiment
+#else if $anchors.format == "h5seurat"
+--anchors-object-file anchors.h5seurat --anchors-format h5seurat
+#end if
+</token>
+<token name="@REFERENCE_OBJ_PREAMBLE@">
+#if $reference.format == 'loom'
+ln -s '$reference.loom_file' reference.loom;
+#else if $reference.format == 'h5seurat'
+ln -s '$reference.h5seurat_file' reference.h5seurat;
+#else if $reference.format == 'anndata'
+## it complains when using links for AnnData...
+cp '$reference.anndata_file' reference.h5ad;
+#end if
+</token>
+<token name="@REFERENCE_OBJECT@">
+#if $reference.format == "anndata"
+--reference-object-file reference.h5ad --reference-format anndata
+#else if $reference.format == "loom"
+--reference-object-file reference.loom --reference-format loom
+#else if $reference.format == "rds_seurat"
+--reference-object-file '$reference.rds_seurat_file' --reference-format seurat
+#else if $reference.format == "rds_sce"
+--reference-object-file '$reference.rds_sce_file' --reference-format singlecellexperiment
+#else if $reference.format == "h5seurat"
+--reference-object-file reference.h5seurat --reference-format h5seurat
+#end if
+</token>
+<token name="@INPUT_OBJS_PREAMBLE@">
+#if $input.format == 'loom'
+#for $i, $fh in enumerate($input.loom_file):
+ln -s '$fh' input.${i}.loom;
+#end for
+#else if $input.format == 'h5seurat'
+#for $i, $fh in enumerate($input.h5seurat_file):
+ln -s '$fh' input.${i}.h5seurat;
+#end for
+#else if $input.format == 'anndata'
+## it complains when using links for AnnData...
+#for $i, $fh in enumerate($input.anndata_file):
+cp '$fh' input.${i}.h5ad;
+#end for
+#end if
+</token>
+<token name="@INPUT_OBJECTS@">
+#if $input.format == "anndata"
+--input-object-files
+#set file_array = [ "input."+str($i)+".h5ad" for $i, $fh in enumerate($input.anndata_file)]
+#set files = ",".join($file_array)
+${files}
+--input-format anndata
+#else if $input.format == "loom"
+--input-object-files
+#set file_array = [ "input."+str($i)+".loom" for $i, $fh in enumerate($input.loom_file)]
+#set files = ",".join($file_array)
+${files}
+--input-format loom
+#else if $input.format == "rds_seurat"
+--input-object-files
+#set file_array = $input.rds_seurat_file
+#set files = ",".join([ str($fh) for $fh in $file_array ])
+${files}
+--input-format seurat
+#else if $input.format == "rds_sce"
+--input-object-files
+#set file_array = $input.rds_sce_file
+#set files = ",".join([ str($fh) for $fh in $file_array ])
+${files}
+--input-format singlecellexperiment
+#else if $input.format == "h5seurat"
+--input-object-files
+#set file_array = [ "input."+str($i)+".h5seurat" for $i, $fh in enumerate($input.h5seurat)]
+#set files = ",".join($file_array)
+${files}
+--input-format h5seurat
+#end if
+</token>
+<token name="@REFERENCE_OBJS_PREAMBLE@">
+#if $reference.format == 'loom'
+#for $i, $fh in enumerate($reference.loom_file):
+ln -s '$fh' reference.${i}.loom;
+#end for
+#else if $reference.format == 'h5seurat'
+#for $i, $fh in enumerate($reference.h5seurat_file):
+ln -s '$fh' reference.${i}.h5seurat;
+#end for
+#else if $reference.format == 'anndata'
+## it complains when using links for AnnData...
+#for $i, $fh in enumerate($reference.anndata_file):
+cp '$fh' reference.${i}.h5ad;
+#end for
+#end if
+</token>
+<token name="@REFERENCE_OBJECTS@">
+#if $reference.format == "anndata" and $reference.anndata_file:
+--reference-object-files
+#set file_array = [ "reference."+str($i)+".h5ad" for $i, $fh in enumerate($reference.anndata_file)]
+#set files = ",".join($file_array)
+${files}
+--reference-format anndata
+#else if $reference.format == "loom" and $reference.loom_file:
+--reference-object-files
+#set file_array = [ "reference."+str($i)+".loom" for $i, $fh in enumerate($reference.loom_file)]
+#set files = ",".join($file_array)
+${files}
+--reference-format loom
+#else if $reference.format == "rds_seurat" and $reference.rds_seurat_file:
+--reference-object-files
+#set files = ",".join([ str($fh) for $fh in $reference.rds_seurat_file ])
+${files}
+--reference-format seurat
+#else if $reference.format == "rds_sce" and $reference.rds_sce_file:
+--reference-object-files
+#set files = ",".join([ str($fh) for $fh in $reference.rds_sce_file ])
+${files}
+--reference-format singlecellexperiment
+#else if $reference.format == "h5seurat" and $reference.h5seurat:
+--reference-object-files
+#set file_array = [ "reference."+str($i)+".h5seurat" for $i, $fh in enumerate($reference.h5seurat)]
+#set files = ",".join($file_array)
+${files}
+--reference-format h5seurat
 #end if
 </token>
 <xml name="output_object_params">
-<param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom">
+<param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment, AnnData or Loom">
 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
+<option value="anndata">AnnData written by Seurat</option>
 <option value="loom">Loom</option>
 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
 </param>
 </xml>
 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
 <filter>format == 'loom'</filter>
 </data>
 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
 <filter>format == 'rds_seurat'</filter>
+</data>
+<data name="anndata_file" format="h5ad" label="${tool.name} on ${on_string}: AnnData from Seurat">
+<filter>format == 'anndata'</filter>
 </data>
 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
 <filter>format == 'rds_sce'</filter>
 </data>
 </xml>
 #else if $format == "rds_sce"
 --output-object-file '$rds_sce_file' --output-format singlecellexperiment
 #end if
 </token>
+<xml name="plot_output_files_format" token_format="png">
+<data label="Seurat ${plot_type.plot_type_selector} on ${on_string}: @FORMAT@ plot" name="plot_out_@FORMAT@" format='@FORMAT@' >
+<filter>plot_format == '@FORMAT@'</filter>
+</data>
+</xml>
+<token name="@OUTPUT_PLOT@">
+#if $plot_format == "png"
+--plot-out '$plot_out_png'
+#else if $plot_format == "pdf"
+--plot-out '$plot_out_pdf'
+#else if $plot_format == "eps"
+--plot-out '$plot_out_eps'
+#else if $plot_format == "ps"
+--plot-out '$plot_out_ps'
+#else if $plot_format == "jpg"
+--plot-out '$plot_out_jpg'
+#else if $plot_format == "tiff"
+--plot-out '$plot_out_tiff'
+#else if $plot_format == "svg"
+--plot-out '$plot_out_svg'
+#end if
+</token>
 <xml name="genes-use-input">
 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
 </xml>
 <xml name="dims-use-input">
 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
 types of single cell data.
 ]]></token>
 <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.
 3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.
 3.1.2_0.0.8: Update metadata parsing
 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
 Find clusters: removed dims-use, k-param, prune-snn.
 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
-EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(github.com/drosofff) and Lea Bellenger(github.com/bellenger-l).
+EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).
-0.0.1: Initial contribution. Maria Doyle (github.com/mblue9).
+0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).
 ]]></token>
 <xml name="citations">
 <citations>
+<citation type="doi">10.1038/s41592-021-01102-w</citation>
 <citation type="doi">10.1038/nbt.4096</citation>
 <citation type="bibtex">
 @misc{r-seurat-scripts.git,
 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
 year = {2018},
 publisher = {GitHub},
 journal = {GitHub repository},
 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
 }
 </citation>
-<citation type="doi">10.1038/s41592-021-01102-w</citation>
 </citations>
 </xml>
 </macros>

Mercurial > repos > ebi-gxa > seurat_scale_data

comparison seurat_macros.xml @ 6:5e9ba303f9e1 draft default tip