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comparison scanpy-read-10x.xml @ 0:572b6e3b2aff draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:11:38 -0400
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-1:000000000000 0:572b6e3b2aff
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0">
3 <description>into hdf5 object handled by scanpy</description>
4 <macros>
5 <import>scanpy_macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${matrix}' matrix.mtx &&
10 ln -s '${genes}' genes.tsv &&
11 ln -s '${barcodes}' barcodes.tsv &&
12 PYTHONIOENCODING=utf-8 scanpy-read-10x.py
13 -d ./
14 -o read_10x.h5
15 -F '${output_format}'
16 -v '${var_names}'
17 ]]></command>
18
19 <inputs>
20 <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/>
21 <param name="genes" type="data" format="tsv,tabular" label="Gene table"/>
22 <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/>
23 <expand macro="output_object_params"/>
24 <param name="var_names" type="select" label="Attribute used as annotation index">
25 <option value="gene_ids" selected="true">Gene ID</option>
26 <option value="gene_symbols">Gene symbol</option>
27 </param>
28 </inputs>
29
30 <outputs>
31 <data name="output_h5" format="h5" from_work_dir="read_10x.h5" label="${tool.name} on ${on_string}: ${output_format}"/>
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="matrix" value="matrix.mtx"/>
37 <param name="genes" value="genes.tsv"/>
38 <param name="barcodes" value="barcodes.tsv"/>
39 <param name="output_format" value="anndata"/>
40 <output name="output_h5" file="read_10x.h5" ftype="h5" compare="sim_size"/>
41 </test>
42 </tests>
43
44 <help><![CDATA[
45 ==========================================================
46 Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)
47 ==========================================================
48
49 The mtx directory should contain:
50
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.
52
53 2) A gene table of at least two columns where the first column gives the gene IDs.
54
55 3) A barcode/cell table of at least one column giving the barcode/cell IDs.
56
57 The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval`
58 with a dataset accession.
59
60
61 @HELP@
62
63 @VERSION_HISTORY@
64 ]]></help>
65 <expand macro="citations"/>
66 </tool>