Mercurial > repos > ebi-gxa > scanpy_read_10x
comparison scanpy-read-10x.xml @ 1:3faf577f3e40 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
author | ebi-gxa |
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date | Mon, 16 Sep 2019 08:19:16 -0400 |
parents | 572b6e3b2aff |
children | f180f7230cdb |
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0:572b6e3b2aff | 1:3faf577f3e40 |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0"> | 2 <tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0"> |
3 <description>into hdf5 object handled by scanpy</description> | 3 <description>into hdf5 object handled by scanpy</description> |
4 <macros> | 4 <macros> |
5 <import>scanpy_macros.xml</import> | 5 <import>scanpy_macros2.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ln -s '${matrix}' matrix.mtx && | 9 ln -s '${matrix}' matrix.mtx && |
10 ln -s '${genes}' genes.tsv && | 10 ln -s '${genes}' genes.tsv && |
11 ln -s '${barcodes}' barcodes.tsv && | 11 ln -s '${barcodes}' barcodes.tsv && |
12 PYTHONIOENCODING=utf-8 scanpy-read-10x.py | 12 PYTHONIOENCODING=utf-8 scanpy-read-10x |
13 -d ./ | 13 --input-10x-mtx ./ |
14 -o read_10x.h5 | 14 --var-names '${var_names}' |
15 -F '${output_format}' | 15 #if $cell_meta: |
16 -v '${var_names}' | 16 --extra-obs '${cell_meta}' |
17 #end if | |
18 #if $gene_meta: | |
19 --extra-var '${gene_meta}' | |
20 #end if | |
21 @OUTPUT_OPTS@ | |
17 ]]></command> | 22 ]]></command> |
18 | 23 |
19 <inputs> | 24 <inputs> |
20 <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/> | 25 <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/> |
21 <param name="genes" type="data" format="tsv,tabular" label="Gene table"/> | 26 <param name="genes" type="data" format="tsv,tabular" label="Gene table"/> |
22 <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/> | 27 <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/> |
28 <param name="cell_meta" type="data" format="tsv,tabular" label="Cell metadata table" optional="true" | |
29 help="Requires a header row and index column that matches the barcode/cell table"/> | |
30 <param name="gene_meta" type="data" format="tsv,tabular" label="Gene metadata table" optional="true" | |
31 help="Requires a header row and index column that matches the gene table"/> | |
23 <expand macro="output_object_params"/> | 32 <expand macro="output_object_params"/> |
24 <param name="var_names" type="select" label="Attribute used as annotation index"> | 33 <param name="var_names" type="select" label="Attribute used as annotation index"> |
25 <option value="gene_ids" selected="true">Gene ID</option> | 34 <option value="gene_ids" selected="true">Gene ID</option> |
26 <option value="gene_symbols">Gene symbol</option> | 35 <option value="gene_symbols">Gene symbol</option> |
27 </param> | 36 </param> |
28 </inputs> | 37 </inputs> |
29 | 38 |
30 <outputs> | 39 <outputs> |
31 <data name="output_h5" format="h5" from_work_dir="read_10x.h5" label="${tool.name} on ${on_string}: ${output_format}"/> | 40 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: ${output_format}"/> |
32 </outputs> | 41 </outputs> |
33 | 42 |
34 <tests> | 43 <tests> |
35 <test> | 44 <test> |
36 <param name="matrix" value="matrix.mtx"/> | 45 <param name="matrix" value="matrix.mtx"/> |
37 <param name="genes" value="genes.tsv"/> | 46 <param name="genes" value="genes.tsv"/> |
38 <param name="barcodes" value="barcodes.tsv"/> | 47 <param name="barcodes" value="barcodes.tsv"/> |
48 <!-- <param name="cell_meta" value=""/> --> | |
39 <param name="output_format" value="anndata"/> | 49 <param name="output_format" value="anndata"/> |
40 <output name="output_h5" file="read_10x.h5" ftype="h5" compare="sim_size"/> | 50 <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/> |
41 </test> | 51 </test> |
42 </tests> | 52 </tests> |
43 | 53 |
44 <help><![CDATA[ | 54 <help><![CDATA[ |
45 ========================================================== | 55 ================================================================= |
46 Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`) | 56 Read 10x-Genomics-formatted mtx directory (`scanpy.read_10x_mtx`) |
47 ========================================================== | 57 ================================================================= |
48 | 58 |
49 The mtx directory should contain: | 59 The mtx directory should contain: |
50 | 60 |
51 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. | 61 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. |
52 | 62 |
53 2) A gene table of at least two columns where the first column gives the gene IDs. | 63 2) A gene table of at least two columns where the first column gives the gene IDs. |
54 | 64 |
55 3) A barcode/cell table of at least one column giving the barcode/cell IDs. | 65 3) A barcode/cell table of at least one column giving the barcode/cell IDs. |
56 | 66 |
57 The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` | 67 The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` with a dataset accession or `Human Cell Atlas Matrix Downloader` with a project name/label/UUID. |
58 with a dataset accession. | 68 |
69 Additionally, cell and/or gene metadata table can be provided as tab-separated text with a header row and an index column that matches the respective barcode/cell and/or gene table. | |
59 | 70 |
60 | 71 |
61 @HELP@ | 72 @HELP@ |
62 | 73 |
63 @VERSION_HISTORY@ | 74 @VERSION_HISTORY@ |