| Previous changeset 0:ef1449a3f358 (2019-10-20) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit d125854376bf1b5c768b8513bc26f197c3373fea |
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modified:
sceasy_convert.xml |
| b |
| diff -r ef1449a3f358 -r f62bc418173f sceasy_convert.xml --- a/sceasy_convert.xml Sun Oct 20 08:47:47 2019 -0400 +++ b/sceasy_convert.xml Mon Oct 21 12:37:29 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy0"> +<tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy1"> <description>a data object between formats</description> <macros> <import>sceasy_macros.xml</import> @@ -16,19 +16,19 @@ Rscript -e 'library(sceasy)' #if $conversion.direction == "loom2sce" - -e 'sce <- sceasy::convertFormat("input.loom", from="loom", to="sce", main_layer_name="${assay_name}")' + -e 'sce <- sceasy::convertFormat("input.loom", from="loom", to="sce", main_layer_name="${conversion.assay_name}")' -e 'saveRDS(sce, "output.rds")' -e 'print(sce)' #else if $conversion.direction == "sce2loom" -e 'sce <- readRDS("input.rds")' - -e 'sceasy::convertFormat(sce, outFile="output.loom", from="sce", to="loom", main_layer="${assay}")' + -e 'sceasy::convertFormat(sce, outFile="output.loom", from="sce", to="loom", main_layer="${conversion.assay}")' #else if $conversion.direction == "sce2anndata" -e 'sce <- readRDS("input.rds")' - -e 'sceasy::convertFormat(sce, outFile="output.h5ad", from="sce", to="anndata", main_layer="${assay}")' + -e 'sceasy::convertFormat(sce, outFile="output.h5ad", from="sce", to="anndata", main_layer="${conversion.assay}")' -e 'print(sce)' #else if $conversion.direction == "seurat2anndata" -e 'srt <- readRDS("input.rds")' - -e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${assay}", main_layer="${dtype}")' + -e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${conversion.assay}", main_layer="${conversion.dtype}")' -e 'print(srt)' #end if ]]></command> |