Mercurial > repos > iuc > sra_tools
comparison sra_macros.xml @ 18:7068f48d0ef9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
author | iuc |
---|---|
date | Mon, 08 Jun 2020 05:49:21 -0400 |
parents | c441583adae5 |
children | 248f85ff0733 |
comparison
equal
deleted
inserted
replaced
17:c441583adae5 | 18:7068f48d0ef9 |
---|---|
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=" "/> |