Mercurial > repos > iuc > anndata_import
comparison import.xml @ 9:499059586799 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 53df027ff1c3c3f580b2cc356887b0c8cce82a94"
author | iuc |
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date | Thu, 23 Sep 2021 18:24:58 +0000 |
parents | ae1e5d9d8972 |
children | 55e35e9203cf |
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8:ae1e5d9d8972 | 9:499059586799 |
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32 && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv' | 32 && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv' |
33 && gzip 'mtx/barcodes.tsv' | 33 && gzip 'mtx/barcodes.tsv' |
34 #end if | 34 #end if |
35 && | 35 && |
36 #else if $hd5_format.in.adata_format == 'umi_tools' | 36 #else if $hd5_format.in.adata_format == 'umi_tools' |
37 gzip '$hd5_format.in.input' | 37 ## avoid gzipping in the inputdir |
38 gzip -c '$hd5_format.in.input' > umi_tools_input.gz | |
38 && | 39 && |
39 #end if | 40 #end if |
40 | 41 |
41 @CMD@ | 42 @CMD@ |
42 | 43 |
93 cache=False, | 94 cache=False, |
94 gex_only=$hd5_format.in.tenx.gex_only) | 95 gex_only=$hd5_format.in.tenx.gex_only) |
95 #end if | 96 #end if |
96 | 97 |
97 #else if $hd5_format.in.adata_format == 'umi_tools' | 98 #else if $hd5_format.in.adata_format == 'umi_tools' |
98 adata = ad.read_umi_tools('${hd5_format.in.input}.gz') | 99 adata = ad.read_umi_tools('umi_tools_input.gz') |
99 #end if | 100 #end if |
100 adata.write('anndata.h5ad') | 101 adata.write('anndata.h5ad') |
101 #end if | 102 #end if |
102 ]]></configfile> | 103 ]]></configfile> |
103 </configfiles> | 104 </configfiles> |