Mercurial > repos > ebi-gxa > sceasy_convert

annotate 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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ef1449a3f358 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 06283e92907321289efca757b97c46c3bd94a2ea-dirty
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="sceasy_convert" name="SCEasy convert" version="@TOOL_VERSION@+galaxy1">
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3 <description>a data object between formats</description>
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4 <macros>
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5 <import>sceasy_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if str($conversion['direction']).startswith("loom")
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10 ln -s ${conversion.input_object_file} input.loom &&
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11 #else if str($conversion['direction']).startswith("anndata")
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12 ln -s ${conversion.input_object_file} input.h5ad &&
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13 #else
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14 ln -s ${conversion.input_object_file} input.rds &&
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15 #end if
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17 Rscript -e 'library(sceasy)'
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18 #if $conversion.direction == "loom2sce"
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19 -e 'sce <- sceasy::convertFormat("input.loom", from="loom", to="sce", main_layer_name="${conversion.assay_name}")'
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20 -e 'saveRDS(sce, "output.rds")'
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21 -e 'print(sce)'
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22 #else if $conversion.direction == "sce2loom"
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23 -e 'sce <- readRDS("input.rds")'
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ebi-gxa
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24 -e 'sceasy::convertFormat(sce, outFile="output.loom", from="sce", to="loom", main_layer="${conversion.assay}")'
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25 #else if $conversion.direction == "sce2anndata"
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26 -e 'sce <- readRDS("input.rds")'
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27 -e 'sceasy::convertFormat(sce, outFile="output.h5ad", from="sce", to="anndata", main_layer="${conversion.assay}")'
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28 -e 'print(sce)'
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29 #else if $conversion.direction == "seurat2anndata"
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30 -e 'srt <- readRDS("input.rds")'
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31 -e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${conversion.assay}", main_layer="${conversion.dtype}")'
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32 -e 'print(srt)'
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33 #end if
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34 ]]></command>
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35
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36 <inputs>
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37 <conditional name="conversion">
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38 <param name="direction" type="select" label="Direction of conversion">
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39 <option value="loom2sce" selected="true">Loom to SingleCellExperiment</option>
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40 <option value="sce2loom">SingleCellExperiment to Loom</option>
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41 <option value="seurat2anndata">Seurat to AnnData</option>
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42 <option value="sce2anndata">SingleCellExperiment to AnnData</option>
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43 </param>
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44 <when value="loom2sce">
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45 <param name="input_object_file" type="data" format="h5" label="Input object in Loom format"/>
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46 <param name="assay_name" type="text" label="Name of the expression matrix to be transferred as">
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47 <option value="counts" selected="true">counts</option>
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48 <option value="logcounts">logcounts</option>
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49 <option value="cpm">cpm</option>
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50 </param>
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51 </when>
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52 <when value="sce2loom">
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53 <param name="input_object_file" type="data" format="rdata" label="Input object in SingleCellExperiment RDS format"/>
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54 <param name="assay" type="text" label="Name of the assay to be transferred as main layer" help="Please make sure the assay exists">
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55 <option value="counts" selected="true">counts</option>
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56 <option value="logcounts">logcounts</option>
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57 <option value="cpm">cpm</option>
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58 </param>
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59 </when>
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60 <when value="sce2anndata">
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61 <param name="input_object_file" type="data" format="rdata" label="Input object in SingleCellExperiment RDS format"/>
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62 <param name="assay" type="text" label="Name of the assay to be transferred as main layer" help="Please make sure the assay exists">
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63 <option value="counts" selected="true">counts</option>
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64 <option value="logcounts">logcounts</option>
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65 <option value="cpm">cpm</option>
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66 </param>
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67 </when>
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68 <when value="seurat2anndata">
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69 <param name="input_object_file" type="data" format="rdata" label="Input object in Seurat RDS format"/>
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70 <param name="assay" type="text" value="RNA" label="Name of the assay to be transferred" help="Please make sure the assay exists"/>
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71 <param name="dtype" type="select" value="RNA" label="Data type of the assay to be transferred" help="Please make sure the data type exists">
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72 <option value="data" selected="true">data</option>
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73 <option value="counts">counts</option>
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74 <option value="scale.data">scale.data</option>
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75 </param>
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76 </when>
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77 </conditional>
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78 </inputs>
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79
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80 <outputs>
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81 <data name="output_sce" format="rdata" from_work_dir="output.rds" label="${tool.name} on ${on_string}: SingleCellExperiment">
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82 <filter>conversion['direction'].endswith('sce')</filter>
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83 </data>
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84 <data name="output_loom" format="h5" from_work_dir="output.loom" label="${tool.name} on ${on_string}: Loom">
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85 <filter>conversion['direction'].endswith('loom')</filter>
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86 </data>
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87 <data name="output_anndata" format="h5" from_work_dir="output.h5ad" label="${tool.name} on ${on_string}: AnnData">
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88 <filter>conversion['direction'].endswith('anndata')</filter>
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89 </data>
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90 </outputs>
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91
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92 <tests>
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93 <test>
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94 <param name="direction" value="loom2sce"/>
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95 <param name="input_object_file" value="input.loom"/>
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96 <output name="output_sce" file="output.rds" ftype="rdata" compare="sim_size"/>
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97 </test>
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98 </tests>
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99
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100 <help><![CDATA[
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101 ===================================================================
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102 Convert scRNA data object between formats `sceasy::convertFormat()`
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103 ===================================================================
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104
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105 Support the following conversion:
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106 * Loom <-> SingleCellExperiment (full)
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107 * SingleCellExperiment -> AnnData (matrix, metadata, reducedDim)
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108 * Seurat -> AnnData (matrix, metadata, reducedDim)
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109
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110 @HELP@
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111
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112 @VERSION_HISTORY@
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113 ]]></help>
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114 <expand macro="citations"/>
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115 </tool>