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comparison 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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1:2e81fbe036b2 2:c3c85b67d118
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.3+galaxy0"> 2 <tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.4+galaxy0">
3 <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description> 3 <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.0.3">hca-matrix-downloader</requirement> 5 <requirement type="package" version="0.0.4">hca-matrix-downloader</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 8
9 hca-matrix-downloader -p '${project}' -o out -f '${matrix_format}' 9 hca-matrix-downloader -p '${project}' -o out -f '${matrix_format}'
10 10
11 #if $species:
12 -s ${species}
13 #end if
11 #if $matrix_format == "mtx": 14 #if $matrix_format == "mtx":
12 && hca-mtx-to-10x out.mtx . 15 && hca-mtx-to-10x out.mtx .
13 && gunzip -c out.mtx/cells.tsv.gz > exp_design.tsv 16 && gunzip -c out.mtx/cells.tsv.gz > exp_design.tsv
14 #end if 17 #end if
15 18
19 <param name="project" type="text" value="Single cell transcriptome analysis of human pancreas" label="Human Cell Atlas project name/label/UUID" help="HCA project identifier, can be project title, project label or project UUID."/> 22 <param name="project" type="text" value="Single cell transcriptome analysis of human pancreas" label="Human Cell Atlas project name/label/UUID" help="HCA project identifier, can be project title, project label or project UUID."/>
20 <param name="matrix_format" type="select" label="Choose the format of matrix to download" help="Matrix Market or Loom"> 23 <param name="matrix_format" type="select" label="Choose the format of matrix to download" help="Matrix Market or Loom">
21 <option value="mtx" selected="true">Matrix Market</option> 24 <option value="mtx" selected="true">Matrix Market</option>
22 <option value="loom">Loom</option> 25 <option value="loom">Loom</option>
23 </param> 26 </param>
27 <param name="species" argument="--species" optional="true" type="text" label="Species to use" help="Certain studies will contain more than one species, in that case, one should be given as input. If you try to download data from such a study, the tool will fail and give you a list in the Std. out of what are the potential species to paste here. This is not needed for most studies that have a single species."/>
24 </inputs> 28 </inputs>
25 29
26 <outputs> 30 <outputs>
27 <data name="matrix_mtx" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string} matrix.mtx"> 31 <data name="matrix_mtx" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string} matrix.mtx">
28 <filter>matrix_format=="mtx"</filter> 32 <filter>matrix_format=="mtx"</filter>
41 </data> 45 </data>
42 </outputs> 46 </outputs>
43 47
44 <tests> 48 <tests>
45 <test> 49 <test>
46 <param name="project" value="Single cell transcriptome analysis of human pancreas"/> 50 <param name="project" value="cddab57b-6868-4be4-806f-395ed9dd635a"/>
47 <param name="matrix_format" value="mtx"/> 51 <param name="matrix_format" value="mtx"/>
48 <output name="matrix_mtx" file="matrix.mtx" ftype="txt"/> 52 <output name="matrix_mtx" md5="0549fc0260eb6974affb115ac80b6e85" ftype="txt"/>
49 <output name="genes_tsv" file="genes.tsv" ftype="tsv"/> 53 <output name="genes_tsv" md5="7e131ba105f713d2f9766d61c246d0da" ftype="tsv"/>
50 <output name="barcode_tsv" file="barcodes.tsv" ftype="tsv"/> 54 <output name="barcode_tsv" md5="327926a684ad8eaee5de8243c32b415c" ftype="tsv"/>
51 <output name="cells_meta_tsv" file="exp_design.tsv" ftype="tsv"/> 55 <output name="cells_meta_tsv" md5="defa674847e3e1877ab1957a3291b28d" ftype="tsv"/>
56 </test>
57 <test>
58 <param name="project" value="f8aa201c-4ff1-45a4-890e-840d63459ca2"/>
59 <param name="matrix_format" value="loom"/>
60 <param name="species" value="homo_sapiens"/>
61 <output name="matrix_loom" md5="9ba6bd109ec271c338251c5519ea9f5d" ftype="h5"/>
52 </test> 62 </test>
53 </tests> 63 </tests>
54 64
55 <help><![CDATA[ 65 <help><![CDATA[
56 =========================================================================== 66 ===========================================================================
59 69
60 The data retrieval tool presented here allows the user to retrieve expression matrices 70 The data retrieval tool presented here allows the user to retrieve expression matrices
61 and metadata for any public experiment available at Human Cell Atlas data portal. 71 and metadata for any public experiment available at Human Cell Atlas data portal.
62 72
63 To use it, simply set the name, or label, or ID for the desired project, which can be 73 To use it, simply set the name, or label, or ID for the desired project, which can be
64 found at the HCA data browser (https://prod.data.humancellatlas.org/explore/projects), 74 found at the HCA data browser (https://data.humancellatlas.org/explore/projects),
65 and select the desired matrix format (Matrix Market or Loom). 75 and select the desired matrix format (Matrix Market or Loom).
76
77 For projects that have more than one organism, one needs to be specified. If none
78 is specified, then the job will fail and the available options to be specified
79 will be listed in the stdout of the job.
66 80
67 Outputs will be: 81 Outputs will be:
68 82
69 - *When "Matrix Market" is seleted, outputs are in 10X-compatible Matrix Market format:* 83 - *When "Matrix Market" is seleted, outputs are in 10X-compatible Matrix Market format:*
70 84
96 metadata table and gene metadata table, in a single HDF5 file with specification defined 110 metadata table and gene metadata table, in a single HDF5 file with specification defined
97 in http://linnarssonlab.org/loompy/format/index.html. 111 in http://linnarssonlab.org/loompy/format/index.html.
98 112
99 **Version history** 113 **Version history**
100 114
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.
116
101 0.0.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Teichmann Lab at Wellcome Sanger Institute and 117 0.0.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Teichmann Lab at Wellcome Sanger Institute and
102 Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. 118 Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
103 119
104 ]]></help> 120 ]]></help>
105 <citations> 121 <citations>
106 <citation type="doi">10.7554/eLife.27041</citation> 122 <citation type="doi">10.7554/eLife.27041</citation>
123 <citation type="doi">10.1101/2020.04.08.032698</citation>
107 </citations> 124 </citations>
108 </tool> 125 </tool>