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comparison macros.xml @ 34:e407b9da183a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 656986ea053baebf194b5311715d7d50a1ac0991
author iuc
date Fri, 17 Nov 2023 10:28:20 +0000
parents 6591f049cf7e
children de0f7e0a3896
comparison
equal deleted inserted replaced
33:6591f049cf7e 34:e407b9da183a
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.0.8</token> 2 <token name="@TOOL_VERSION@">3.0.8</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">22.01</token> 4 <token name="@PROFILE@">22.01</token>
5 <xml name="edam_ontology"> 5 <xml name="edam_ontology">
6 <edam_topics> 6 <edam_topics>
7 <edam_topic>topic_0622</edam_topic> <!-- Genomics --> 7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics --> 8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
34 </xrefs> 34 </xrefs>
35 </xml> 35 </xml>
36 <token name="@COPY_CONFIGFILE@"><![CDATA[ 36 <token name="@COPY_CONFIGFILE@"><![CDATA[
37 mkdir -p ~/.ncbi && 37 mkdir -p ~/.ncbi &&
38 cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg && 38 cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
39 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
40 vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
41 vdb-config -s "/repository/user/default-path=\$PWD" &&
42 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
43 vdb-config -s /http/timeout/read=10000 &&
44 ]]></token> 39 ]]></token>
45 <token name="@SET_ACCESSIONS@"><![CDATA[ 40 <token name="@SET_ACCESSIONS@"><![CDATA[
46 #if $input.input_select == "sra_file": 41 #if $input.input_select == "sra_file":
47 acc='${input.sra_file.name}' && 42 acc='${input.sra_file.name}' &&
48 ln -s '${input.sra_file}' "\$acc" && 43 ln -s '${input.sra_file}' "\$acc" &&
67 <configfile name="user_settings_mkfg"><![CDATA[ 62 <configfile name="user_settings_mkfg"><![CDATA[
68 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec" 63 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
69 /config/default = "false" 64 /config/default = "false"
70 /libs/temp_cache = "." 65 /libs/temp_cache = "."
71 /tools/prefetch/download_to_cache = "false" 66 /tools/prefetch/download_to_cache = "false"
67 /http/timeout/read = "1000"
68 /repository/user/main/public/root = "."
69 /repository/user/ad/public/root = "."
70 /repository/user/default-path = "."
71 /repository/user/main/public/root = "."
72 ]]></configfile> 72 ]]></configfile>
73 </configfiles> 73 </configfiles>
74 </macro> 74 </macro>
75 <macro name="sanitize_query"> 75 <macro name="sanitize_query">
76 <sanitizer> 76 <sanitizer>