Mercurial > repos > iuc > sra_tools

comparison sra_macros.xml @ 19:248f85ff0733 draft

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"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
comparison
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18:7068f48d0ef9 19:248f85ff0733
17 vdb-config -s "/repository/user/main/public/root=\$PWD" && 17 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
18 vdb-config -s /http/timeout/read=10000 && 18 vdb-config -s /http/timeout/read=10000 &&
19 ]]></token> 19 ]]></token>
20 <token name="@SET_ACCESSIONS@"><![CDATA[ 20 <token name="@SET_ACCESSIONS@"><![CDATA[
21 #if $input.input_select=="file_list": 21 #if $input.input_select=="file_list":
22 for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ; 22 #if $input.file_list.is_of_type('sra_manifest.tabular'):
23 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
24 cut -f $column '$input.file_list'| tail -n +2 > "manifest" &&
25 #else
26 ln -s '$input.file_list' > manifest &&
27 #end if
28 for acc in `@ACCESSIONS_FROM_FILE@ manifest` ;
23 do ( 29 do (
24 #elif $input.input_select=="accession_number": 30 #elif $input.input_select=="accession_number":
25 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( 31 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
26 #end if 32 #end if
27 ]]></token> 33 ]]></token>