Mercurial > repos > iuc > sra_tools

comparison sra_macros.xml @ 22:751a694ec620 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1db2b3ee758847b8b63f58fb2075961003ff8c22"
author iuc
date Mon, 20 Jul 2020 07:27:41 -0400
parents 494b2ec08162
children 653e89d73fc4
comparison
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21:494b2ec08162 22:751a694ec620
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,}$" ] && (