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add anndata2seurat conversion #265

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add anndata2seurat conversion #265

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17 changes: 16 additions & 1 deletion tools/tertiary-analysis/sceasy/sceasy_convert.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,10 @@
-e 'srt <- readRDS("input.rds")'
-e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${conversion.assay}", main_layer="${conversion.dtype}")'
-e 'print(srt)'
#else if $conversion.direction == "anndata2seurat"
-e 'srt <- sceasy::convertFormat("input.h5ad", from="anndata", to="seurat", main_layer="${conversion.assay}")'
-e 'saveRDS(srt, "output.rds")'
-e 'print(srt)'
#end if
]]></command>

Expand Down Expand Up @@ -74,6 +78,14 @@
<option value="scale.data">scale.data</option>
</param>
</when>
<when value="anndata2seurat">
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I think that you also need to add an option in the conditional.param block (lines 42 to 46) for anndata2seurat.

<param name="input_object_file" type="data" format="h5ad" label="Input object in AnnData format"/>
<param name="assay" type="text" value="RNA" label="Name of assay in Seurat object to store expression values" help="Please make sure the assay exists"/>
<option value="counts" selected="true">counts</option>
<option value="logcounts">logcounts</option>
<option value="cpm">cpm</option>
</param>
</when>
</conditional>
</inputs>

Expand All @@ -87,6 +99,9 @@
<data name="output_anndata" format="h5" from_work_dir="output.h5ad" label="${tool.name} on ${on_string}: AnnData">
<filter>conversion['direction'].endswith('anndata')</filter>
</data>
<data name="output_seurat" format="rdata" from_work_dir="output.rds" label="${tool.name} on ${on_string}: Seurat">
<filter>conversion['direction'].endswith('seurat')</filter>
</data>
</outputs>

<tests>
Expand All @@ -105,7 +120,7 @@ Convert scRNA data object between formats `sceasy::convertFormat()`
Support the following conversion:
* Loom <-> SingleCellExperiment (full)
* SingleCellExperiment -> AnnData (matrix, metadata, reducedDim)
* Seurat -> AnnData (matrix, metadata, reducedDim)
* Seurat <-> AnnData (matrix, metadata, reducedDim)

@HELP@

Expand Down