Mercurial > repos > ebi-gxa > hca_matrix_downloader

annotate matrix-service.xml @ 2:c3c85b67d118 draft default tip

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 81ed2d7aaad0f5536d835e75e483c39c3984d565"
author ebi-gxa
date Sun, 27 Dec 2020 00:00:19 +0000
parents 2e81fbe036b2
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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="v0.0.4+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="0.0.4">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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8
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9 hca-matrix-downloader -p '${project}' -o out -f '${matrix_format}'
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11 #if $species:
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12 -s ${species}
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13 #end if
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14 #if $matrix_format == "mtx":
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15 && hca-mtx-to-10x out.mtx .
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16 && gunzip -c out.mtx/cells.tsv.gz > exp_design.tsv
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17 #end if
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19 ]]></command>
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21 <inputs>
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22 <param name="project" type="text" value="Single cell transcriptome analysis of human pancreas" label="Human Cell Atlas project name/label/UUID" help="HCA project identifier, can be project title, project label or project UUID."/>
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23 <param name="matrix_format" type="select" label="Choose the format of matrix to download" help="Matrix Market or Loom">
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24 <option value="mtx" selected="true">Matrix Market</option>
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25 <option value="loom">Loom</option>
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26 </param>
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27 <param name="species" argument="--species" optional="true" type="text" label="Species to use" help="Certain studies will contain more than one species, in that case, one should be given as input. If you try to download data from such a study, the tool will fail and give you a list in the Std. out of what are the potential species to paste here. This is not needed for most studies that have a single species."/>
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28 </inputs>
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30 <outputs>
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31 <data name="matrix_mtx" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string} matrix.mtx">
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32 <filter>matrix_format=="mtx"</filter>
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33 </data>
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34 <data name="genes_tsv" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string} genes.tsv">
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35 <filter>matrix_format=="mtx"</filter>
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36 </data>
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37 <data name="barcode_tsv" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string} barcodes.tsv">
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38 <filter>matrix_format=="mtx"</filter>
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39 </data>
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40 <data name="cells_meta_tsv" format="tsv" from_work_dir="exp_design.tsv" label="${tool.name} on ${on_string} exp_design.tsv">
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41 <filter>matrix_format=="mtx"</filter>
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42 </data>
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43 <data name="matrix_loom" format="h5" from_work_dir="out.loom" label="${tool.name} on ${on_string} matrix.loom">
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44 <filter>matrix_format=="loom"</filter>
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45 </data>
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46 </outputs>
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47
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48 <tests>
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49 <test>
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50 <param name="project" value="cddab57b-6868-4be4-806f-395ed9dd635a"/>
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51 <param name="matrix_format" value="mtx"/>
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52 <output name="matrix_mtx" md5="0549fc0260eb6974affb115ac80b6e85" ftype="txt"/>
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53 <output name="genes_tsv" md5="7e131ba105f713d2f9766d61c246d0da" ftype="tsv"/>
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54 <output name="barcode_tsv" md5="327926a684ad8eaee5de8243c32b415c" ftype="tsv"/>
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55 <output name="cells_meta_tsv" md5="defa674847e3e1877ab1957a3291b28d" ftype="tsv"/>
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56 </test>
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57 <test>
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58 <param name="project" value="f8aa201c-4ff1-45a4-890e-840d63459ca2"/>
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59 <param name="matrix_format" value="loom"/>
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60 <param name="species" value="homo_sapiens"/>
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61 <output name="matrix_loom" md5="9ba6bd109ec271c338251c5519ea9f5d" ftype="h5"/>
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62 </test>
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63 </tests>
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64
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65 <help><![CDATA[
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66 ===========================================================================
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67 Down expression matrix from HCA projects using HCA DCP's matrix service API
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68 ===========================================================================
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69
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70 The data retrieval tool presented here allows the user to retrieve expression matrices
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71 and metadata for any public experiment available at Human Cell Atlas data portal.
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72
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73 To use it, simply set the name, or label, or ID for the desired project, which can be
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74 found at the HCA data browser (https://data.humancellatlas.org/explore/projects),
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75 and select the desired matrix format (Matrix Market or Loom).
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76
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77 For projects that have more than one organism, one needs to be specified. If none
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78 is specified, then the job will fail and the available options to be specified
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79 will be listed in the stdout of the job.
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80
0
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81 Outputs will be:
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82
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83 - *When "Matrix Market" is seleted, outputs are in 10X-compatible Matrix Market format:*
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84
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85 1. **Matrix (txt):**
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86
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87 Contains the expression values for genes (rows) and cells (columns) in raw counts. This
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88 text file is formatted as a Matrix Market file, and as such it is accompanied by separate
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89 files for the gene identifiers and the cells identifiers.
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90
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91 2. **Genes (tsv):**
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92
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93 Identifiers (column repeated) for the genes present in the matrix of expression,
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94 in the same order as the matrix rows.
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95
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96 3. **Barcodes (tsv):**
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97
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98 Identifiers for the cells of the data matrix. The file is ordered to match the columns
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99 of the matrix.
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100
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101 4. **Experiment Design file (tsv):**
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102
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103 Contains metadata for the different cells of the experiment.
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104
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105 - *When "Loom" is selected, output is a single Loom HDF5 file:*
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106
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107 1. **Loom (h5):**
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108
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109 Contains expression values for genes (rows) and cells (columns) in raw counts, cell
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110 metadata table and gene metadata table, in a single HDF5 file with specification defined
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111 in http://linnarssonlab.org/loompy/format/index.html.
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112
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113 **Version history**
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114
2
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115 0.0.4+galaxy0: Retrieves data from EBI FTP until an equivalent Matrix service for DCP 2.0 is established. Deals with multi organisms studies.
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116
0
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117 0.0.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Teichmann Lab at Wellcome Sanger Institute and
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118 Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
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119
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120 ]]></help>
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121 <citations>
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122 <citation type="doi">10.7554/eLife.27041</citation>
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123 <citation type="doi">10.1101/2020.04.08.032698</citation>
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124 </citations>
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125 </tool>