Mercurial > repos > iuc > sra_tools

diff sra_macros.xml @ 18:c8d04fc889f2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
author iuc
date Mon, 06 Jul 2020 22:18:55 +0000
parents 37f09413ddbf
children adc510b2288d
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line diff
--- a/sra_macros.xml	Mon Jun 08 09:48:56 2020 +0000
+++ b/sra_macros.xml	Mon Jul 06 22:18:55 2020 +0000
@@ -19,7 +19,13 @@
     ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select=="file_list":
-            for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
+            #if $input.file_list.is_of_type('sra_manifest.tabular'):
+                #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
+                cut -f $column '$input.file_list'| tail -n +2 > "manifest" &&
+            #else
+                ln -s '$input.file_list' manifest &&
+            #end if
+            for acc in `@ACCESSIONS_FROM_FILE@ manifest` ;
             do (
         #elif $input.input_select=="accession_number":
             acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (