Mercurial > repos > ebi-gxa > retrieve_scxa

annotate retrieve-scxa.xml @ 1:cc21614b6693 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 7bf75360bdf687f987e706c3e48667931eaed0ce-dirty
author ebi-gxa
date Tue, 13 Aug 2019 05:36:12 -0400
parents cd6b80f62fcc
children 72b6e1747e37
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.2+galaxy2">
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3 <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
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4 <requirements>
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5 <requirement type="package" version="1.20.1">wget</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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9 #if str($matrix_type) == "tpm":
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11 wget -O exp_quant.zip
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12 'https://www.ebi.ac.uk/gxa/sc/experiment/${accession}/download/zip?fileType=quantification-filtered&accessKey=' &&
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13 unzip exp_quant.zip;
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14 mv '${accession}'.expression_tpm.mtx ${matrix_mtx} &&
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15 awk '{OFS="\t"; print \$2,\$2}' '${accession}'.expression_tpm.mtx_rows > ${genes_tsv} &&
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16 cut -f2 '${accession}'.expression_tpm.mtx_cols > ${barcode_tsv};
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18 #else if str($matrix_type) == "raw":
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20 wget -O ${matrix_mtx} 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx';
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21 wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_cols' | cut -f2 > ${barcode_tsv};
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22 wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.decorated.mtx_rows' |
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23 awk -F'\t' '{ if (length($2) == 0) { print $1"\t"$1 } else { print $0 } }' > ${genes_tsv};
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25 #end if
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27 wget -O exp_design.tsv
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28 'https://www.ebi.ac.uk/gxa/sc/experiment/${accession}/download?fileType=experiment-design&accessKey=';
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30 ]]></command>
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32 <inputs>
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33 <param name="accession" type="text" value="E-GEOD-100058" label="SC-Atlas experiment accession" help="EBI Single Cell Atlas accession for the experiment that you want to retrieve."/>
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34 <param name="matrix_type" type="select" label="Choose the type of matrix to download" help="Raw filtered counts or (non-filtered) TPMs">
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35 <option value="raw" selected="true">Raw filtered counts</option>
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36 <option value="tpm">TPMs</option>
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37 </param>
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38 </inputs>
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39
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40 <outputs>
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41 <data name="matrix_mtx" format="txt" label="${tool.name} on ${on_string} ${accession} matrix.mtx (${matrix_type.value_label})"/>
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42 <data name="genes_tsv" format="tsv" label="${tool.name} on ${on_string} ${accession} genes.tsv (${matrix_type.value_label})"/>
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43 <data name="barcode_tsv" format="tsv" label="${tool.name} on ${on_string} ${accession} barcodes.tsv (${matrix_type.value_label})"/>
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44 <data name="design_tsv" format="tsv" from_work_dir="exp_design.tsv" label="${tool.name} on ${on_string} ${accession} exp_design.tsv"/>
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <param name="accession" value="E-GEOD-100058"/>
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50 <param name="matrix_type" value="tpm"/>
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51 <output name="matrix_mtx" file="E-GEOD-100058.expression_tpm.mtx" ftype="txt"/>
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52 <output name="genes_tsv" file="E-GEOD-100058.genes.tsv" ftype="tsv"/>
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53 <output name="barcode_tsv" file="E-GEOD-100058.barcodes.tsv" ftype="tsv"/>
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54 <output name="design_tsv" file="E-GEOD-100058.exp_design.tsv" ftype="tsv"/>
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55 </test>
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56 </tests>
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57
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58 <help><![CDATA[
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59 =================================================================================
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60 Gene expression analysis in single cells across species and biological conditions
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61 =================================================================================
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62
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63 Single Cell Expression Atlas supports research in single cell transcriptomics.
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64 The Atlas annotates publicly available single cell RNA-Seq experiments with
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65 ontology identifiers and re-analyses them using standardised pipelines available
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66 through iRAP, our RNA-Seq analysis toolkit. The browser enables visualisation of
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67 clusters of cells, their annotations and supports searches for gene expression
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68 within and across studies.
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69
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70 For more information check https://www.ebi.ac.uk/gxa/sc/home
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71
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72 EBI SCXA Data Retrieval
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73 -----------------------
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74
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75 The data retrieval tool presented here allows the user to retrieve expression matrices
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76 and metadata for any public experiment available at EBI Single Cell Expression Atlas.
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78 To use it, simply set the accession for the desired experiment and choose the type of
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79 matrix that you want to download:
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80
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81 :Raw filtered counts:
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82 This should be the default choice for running clustering and another analysis
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83 methods where you will introduce scaling and normalization of the data. The filtering
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84 is based on the quality control applied by iRAP prior to pseudo-alignment and quantification.
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85
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86 :TPMs:
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87 TPM stands for Transcripts Per Kilobase Million, and as the name implies, this has been
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88 already normalized/scaled. You should keep this in mind when using this data
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89 on methods that will try to normalise data as part of their procedure. Due to technical
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90 particularities in the current Atlas SC pipeline, TPMs available here are not filtered.
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91 **Note: droplet databases won't have TPM data**
0
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92
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93 Outputs will be:
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94
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95 :Matrix (txt):
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96 Contains the expression values for genes (rows) and samples/runs/cells (columns),
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97 in either raw filtered counts or filtered tpms depending on the choice made. This
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98 text file is formatted as a Matrix Market file, and as such it is accompanied by
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99 separate files for the gene identifiers and the samples/runs/cells identifiers.
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100
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101 :Genes (tsv):
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102 Identifiers (column repeated) for the genes present in the matrix of expression,
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103 in the same order as the matrix rows.
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104
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105 :Barcodes (tsv):
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106 Identifiers for the cells, samples or runs of the data matrix. The file is ordered
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107 to match the columns of the matrix.
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108
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109 :Experiment Design file (tsv):
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110 Contains metadata for the different cells/samples/runs of the experiment.
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111 Please note that this file is generated before the filtering step, and while not
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112 often, it might be the case that it contains more cells/samples/runs than the matrix.
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113
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114 ]]></help>
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115 <citations>
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116 <citation type="doi">10.1093/nar/gkv1045</citation>
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117 </citations>
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118 </tool>