Mercurial > repos > iuc > anndata_import

changeset 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
files import.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/import.xml	Fri Feb 19 23:48:32 2021 +0000
+++ b/import.xml	Thu Sep 23 18:20:25 2021 +0000
@@ -34,7 +34,8 @@
         #end if
         &&
     #else if $hd5_format.in.adata_format == 'umi_tools'
-        gzip '$hd5_format.in.input'
+        ## avoid gzipping in the inputdir
+        gzip -c '$hd5_format.in.input' > umi_tools_input.gz
         &&
     #end if
 
@@ -95,7 +96,7 @@
         #end if
 
     #else if $hd5_format.in.adata_format == 'umi_tools'
-adata = ad.read_umi_tools('${hd5_format.in.input}.gz')
+adata = ad.read_umi_tools('umi_tools_input.gz')
     #end if
 adata.write('anndata.h5ad')
 #end if