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comparison sra_macros.xml @ 17:37f09413ddbf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
author iuc
date Mon, 08 Jun 2020 09:48:56 +0000
parents f61761f373ea
children c8d04fc889f2
comparison
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16:f61761f373ea 17:37f09413ddbf
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.10.4</token> 2 <token name="@VERSION@">2.10.7</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="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
7 <token name="@CONFIGURE_TIMEOUT@"><![CDATA[
8 vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true &&
9 ]]></token>
10 <token name="@CONFIGURE_RETRY@"><![CDATA[ 7 <token name="@CONFIGURE_RETRY@"><![CDATA[
11 export SRA_PREFETCH_RETRIES=3 && 8 export SRA_PREFETCH_RETRIES=3 &&
12 export SRA_PREFETCH_ATTEMPT=1 && 9 export SRA_PREFETCH_ATTEMPT=1 &&
10 ]]></token>
11 <token name="@COPY_CONFIGFILE@"><![CDATA[
12 mkdir -p ~/.ncbi &&
13 cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
14 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
15 vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
16 vdb-config -s "/repository/user/default-path=\$PWD" &&
17 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
18 vdb-config -s /http/timeout/read=10000 &&
13 ]]></token> 19 ]]></token>
14 <token name="@SET_ACCESSIONS@"><![CDATA[ 20 <token name="@SET_ACCESSIONS@"><![CDATA[
15 #if $input.input_select=="file_list": 21 #if $input.input_select=="file_list":
16 for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ; 22 for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
17 do ( 23 do (
20 #end if 26 #end if
21 ]]></token> 27 ]]></token>
22 28
23 <macro name="requirements"> 29 <macro name="requirements">
24 <requirements> 30 <requirements>
25 <requirement type="package" version="2.10.3">sra-tools</requirement> 31 <requirement type="package" version="@VERSION@">sra-tools</requirement>
26 <requirement type="package" version="2.3.4">pigz</requirement> 32 <requirement type="package" version="2.3.4">pigz</requirement>
27 <yield/> 33 <yield/>
28 </requirements> 34 </requirements>
35 </macro>
36 <macro name="configfile_hack">
37 <configfiles>
38 <configfile name="user_settings_mkfg"><![CDATA[
39 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
40 /config/default = "false"
41 /libs/temp_cache = "."
42 /tools/prefetch/download_to_cache = "false"
43 ]]></configfile>
44 </configfiles>
29 </macro> 45 </macro>
30 <macro name="sanitize_query"> 46 <macro name="sanitize_query">
31 <sanitizer> 47 <sanitizer>
32 <valid initial="string.printable"> 48 <valid initial="string.printable">
33 <remove value=" "/> 49 <remove value=" "/>