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
date Mon, 16 Sep 2019 08:19:16 -0400
parents 572b6e3b2aff
children f180f7230cdb
comparison
equal deleted inserted replaced
0:572b6e3b2aff 1:3faf577f3e40
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@