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comparison sra_macros.xml @ 17:c441583adae5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
author iuc
date Wed, 29 Apr 2020 12:12:23 -0400
parents aad3885b3216
children 7068f48d0ef9
comparison
equal deleted inserted replaced
16:aad3885b3216 17:c441583adae5
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.10.4</token> 2 <token name="@VERSION@">2.10.4</token>
3 <token name="@ACCESSIONS_FROM_FILE@"> 3 <token name="@ACCESSIONS_FROM_FILE@">
4 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$' 4 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
5 </token> 5 </token>
6 <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
6 <token name="@CONFIGURE_TIMEOUT@"><![CDATA[ 7 <token name="@CONFIGURE_TIMEOUT@"><![CDATA[
7 vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true && 8 vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true &&
9 ]]></token>
10 <token name="@CONFIGURE_RETRY@"><![CDATA[
11 export SRA_PREFETCH_RETRIES=3 &&
12 export SRA_PREFETCH_ATTEMPT=1 &&
8 ]]></token> 13 ]]></token>
9 <token name="@SET_ACCESSIONS@"><![CDATA[ 14 <token name="@SET_ACCESSIONS@"><![CDATA[
10 #if $input.input_select=="file_list": 15 #if $input.input_select=="file_list":
11 for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ; 16 for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
12 do ( 17 do (
16 ]]></token> 21 ]]></token>
17 22
18 <macro name="requirements"> 23 <macro name="requirements">
19 <requirements> 24 <requirements>
20 <requirement type="package" version="2.10.3">sra-tools</requirement> 25 <requirement type="package" version="2.10.3">sra-tools</requirement>
26 <requirement type="package" version="2.3.4">pigz</requirement>
21 <yield/> 27 <yield/>
22 </requirements> 28 </requirements>
23 </macro> 29 </macro>
24 <macro name="sanitize_query"> 30 <macro name="sanitize_query">
25 <sanitizer> 31 <sanitizer>