Mercurial > repos > iuc > anndata_import

comparison import.xml @ 9:260ecac7539b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 53df027ff1c3c3f580b2cc356887b0c8cce82a94"
author iuc
date Thu, 23 Sep 2021 18:20:25 +0000
parents ed285e2fbe1b
children 7d13dd31b782
comparison
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8:ed285e2fbe1b 9:260ecac7539b
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>