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comparison sceasy_convert.xml @ 1:f62bc418173f draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit d125854376bf1b5c768b8513bc26f197c3373fea
author ebi-gxa
date Mon, 21 Oct 2019 12:37:29 -0400
parents ef1449a3f358
children
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0:ef1449a3f358 1:f62bc418173f
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy1">
3 <description>a data object between formats</description> 3 <description>a data object between formats</description>
4 <macros> 4 <macros>
5 <import>sceasy_macros.xml</import> 5 <import>sceasy_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
14 ln -s ${conversion.input_object_file} input.rds && 14 ln -s ${conversion.input_object_file} input.rds &&
15 #end if 15 #end if
16 16
17 Rscript -e 'library(sceasy)' 17 Rscript -e 'library(sceasy)'
18 #if $conversion.direction == "loom2sce" 18 #if $conversion.direction == "loom2sce"
19 -e 'sce <- sceasy::convertFormat("input.loom", from="loom", to="sce", main_layer_name="${assay_name}")' 19 -e 'sce <- sceasy::convertFormat("input.loom", from="loom", to="sce", main_layer_name="${conversion.assay_name}")'
20 -e 'saveRDS(sce, "output.rds")' 20 -e 'saveRDS(sce, "output.rds")'
21 -e 'print(sce)' 21 -e 'print(sce)'
22 #else if $conversion.direction == "sce2loom" 22 #else if $conversion.direction == "sce2loom"
23 -e 'sce <- readRDS("input.rds")' 23 -e 'sce <- readRDS("input.rds")'
24 -e 'sceasy::convertFormat(sce, outFile="output.loom", from="sce", to="loom", main_layer="${assay}")' 24 -e 'sceasy::convertFormat(sce, outFile="output.loom", from="sce", to="loom", main_layer="${conversion.assay}")'
25 #else if $conversion.direction == "sce2anndata" 25 #else if $conversion.direction == "sce2anndata"
26 -e 'sce <- readRDS("input.rds")' 26 -e 'sce <- readRDS("input.rds")'
27 -e 'sceasy::convertFormat(sce, outFile="output.h5ad", from="sce", to="anndata", main_layer="${assay}")' 27 -e 'sceasy::convertFormat(sce, outFile="output.h5ad", from="sce", to="anndata", main_layer="${conversion.assay}")'
28 -e 'print(sce)' 28 -e 'print(sce)'
29 #else if $conversion.direction == "seurat2anndata" 29 #else if $conversion.direction == "seurat2anndata"
30 -e 'srt <- readRDS("input.rds")' 30 -e 'srt <- readRDS("input.rds")'
31 -e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${assay}", main_layer="${dtype}")' 31 -e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${conversion.assay}", main_layer="${conversion.dtype}")'
32 -e 'print(srt)' 32 -e 'print(srt)'
33 #end if 33 #end if
34 ]]></command> 34 ]]></command>
35 35
36 <inputs> 36 <inputs>