Mercurial > repos > ebi-gxa > hca_matrix_downloader

annotate matrix-service.xml @ 0:c127d4124583 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 67729956c77554abbaf1d4fd0edf19215eff28da-dirty
author ebi-gxa
date Tue, 02 Jul 2019 11:10:16 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.2+galaxy0">
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3 <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description>
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4 <requirements>
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5 <requirement type="package" version="0.0.2">hca-matrix-downloader</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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9 hca-matrix-downloader -p '${project}' -f mtx -o out -f '${matrix_format}'
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11 #if $matrix_format == "mtx":
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12 && hca-mtx-to-10x out.mtx .
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13 && gunzip -c out.mtx/cells.tsv.gz > exp_design.tsv
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14 #end if
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16 ]]></command>
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18 <inputs>
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19 <param name="project" type="text" value="Single cell transcriptome analysis of human pancreas" label="Human Cell Atlas project name/label/UUID" help="HCA project identifier, can be project title, project label or project UUID."/>
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20 <param name="matrix_format" type="select" label="Choose the format of matrix to download" help="Matrix Market or Loom">
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21 <option value="mtx" selected="true">Matrix Market</option>
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22 <option value="loom">Loom</option>
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23 </param>
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24 </inputs>
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25
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26 <outputs>
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27 <data name="matrix_mtx" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string} matrix.mtx">
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28 <filter>matrix_format=="mtx"</filter>
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29 </data>
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30 <data name="genes_tsv" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string} genes.tsv">
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31 <filter>matrix_format=="mtx"</filter>
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32 </data>
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33 <data name="barcode_tsv" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string} barcodes.tsv">
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34 <filter>matrix_format=="mtx"</filter>
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35 </data>
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36 <data name="cells_meta_tsv" format="tsv" from_work_dir="exp_design.tsv" label="${tool.name} on ${on_string} exp_design.tsv">
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37 <filter>matrix_format=="mtx"</filter>
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38 </data>
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39 <data name="matrix_loom" format="h5" from_work_dir="out.loom" label="${tool.name} on ${on_string} matrix.loom">
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40 <filter>matrix_format=="loom"</filter>
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41 </data>
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42 </outputs>
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43
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44 <tests>
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45 <test>
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46 <param name="project" value="Single cell transcriptome analysis of human pancreas"/>
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47 <param name="matrix_format" value="mtx"/>
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48 <output name="matrix_mtx" file="matrix.mtx" ftype="txt"/>
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49 <output name="genes_tsv" file="genes.tsv" ftype="tsv"/>
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50 <output name="barcode_tsv" file="barcodes.tsv" ftype="tsv"/>
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51 <output name="cells_meta_tsv" file="exp_design.tsv" ftype="tsv"/>
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52 </test>
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53 </tests>
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54
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55 <help><![CDATA[
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56 ===========================================================================
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57 Down expression matrix from HCA projects using HCA DCP's matrix service API
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58 ===========================================================================
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59
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60 The data retrieval tool presented here allows the user to retrieve expression matrices
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61 and metadata for any public experiment available at Human Cell Atlas data portal.
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62
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63 To use it, simply set the name, or label, or ID for the desired project, which can be
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64 found at the HCA data browser (https://prod.data.humancellatlas.org/explore/projects),
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65 and select the desired matrix format (Matrix Market or Loom).
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66
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67 Outputs will be:
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68
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69 - *When "Matrix Market" is seleted, outputs are in 10X-compatible Matrix Market format:*
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70
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71 1. **Matrix (txt):**
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72
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73 Contains the expression values for genes (rows) and cells (columns) in raw counts. This
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74 text file is formatted as a Matrix Market file, and as such it is accompanied by separate
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75 files for the gene identifiers and the cells identifiers.
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76
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77 2. **Genes (tsv):**
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78
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79 Identifiers (column repeated) for the genes present in the matrix of expression,
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80 in the same order as the matrix rows.
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81
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82 3. **Barcodes (tsv):**
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83
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84 Identifiers for the cells of the data matrix. The file is ordered to match the columns
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85 of the matrix.
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86
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87 4. **Experiment Design file (tsv):**
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88
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89 Contains metadata for the different cells of the experiment.
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90
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91 - *When "Loom" is selected, output is a single Loom HDF5 file:*
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92
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93 1. **Loom (h5):**
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94
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95 Contains expression values for genes (rows) and cells (columns) in raw counts, cell
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96 metadata table and gene metadata table, in a single HDF5 file with specification defined
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97 in http://linnarssonlab.org/loompy/format/index.html.
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98
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99 **Version history**
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100
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101 0.0.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Teichmann Lab at Wellcome Sanger Institute and
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102 Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
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103
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104 ]]></help>
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105 <citations>
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106 <citation type="doi">10.7554/eLife.27041</citation>
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107 </citations>
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108 </tool>