Mercurial > repos > iuc > sra_tools
comparison sra_macros.xml @ 20:964579f93c54 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ec1cc6c0c290e9931780ea128bb48caac37977db"
author | iuc |
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date | Wed, 01 Jul 2020 17:48:02 -0400 |
parents | 248f85ff0733 |
children | 494b2ec08162 |
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19:248f85ff0733 | 20:964579f93c54 |
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21 #if $input.input_select=="file_list": | 21 #if $input.input_select=="file_list": |
22 #if $input.file_list.is_of_type('sra_manifest.tabular'): | 22 #if $input.file_list.is_of_type('sra_manifest.tabular'): |
23 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1 | 23 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1 |
24 cut -f $column '$input.file_list'| tail -n +2 > "manifest" && | 24 cut -f $column '$input.file_list'| tail -n +2 > "manifest" && |
25 #else | 25 #else |
26 ln -s '$input.file_list' > manifest && | 26 ln -s '$input.file_list' manifest && |
27 #end if | 27 #end if |
28 for acc in `@ACCESSIONS_FROM_FILE@ manifest` ; | 28 for acc in `@ACCESSIONS_FROM_FILE@ manifest` ; |
29 do ( | 29 do ( |
30 #elif $input.input_select=="accession_number": | 30 #elif $input.input_select=="accession_number": |
31 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( | 31 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( |