Mercurial > repos > iuc > sra_tools
diff sra_macros.xml @ 19:248f85ff0733 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1"
author | iuc |
---|---|
date | Tue, 23 Jun 2020 17:18:45 -0400 |
parents | 7068f48d0ef9 |
children | 964579f93c54 |
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--- a/sra_macros.xml Mon Jun 08 05:49:21 2020 -0400 +++ b/sra_macros.xml Tue Jun 23 17:18:45 2020 -0400 @@ -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,}$" ] && (