comparison macros.xml @ 34:e407b9da183a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 656986ea053baebf194b5311715d7d50a1ac0991

33:6591f049cf7e

<macros>
    <token name="@TOOL_VERSION@">3.0.8</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->

        </xrefs>
    </xml>
    <token name="@COPY_CONFIGFILE@"><![CDATA[
        mkdir -p ~/.ncbi &&
        cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
        vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
        vdb-config -s "/repository/user/default-path=\$PWD" &&
        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
        vdb-config -s /http/timeout/read=10000 &&
    ]]></token>
    <token name="@SET_ACCESSIONS@"><![CDATA[
        #if $input.input_select == "sra_file":
            acc='${input.sra_file.name}' &&
            ln -s '${input.sra_file}' "\$acc" &&

            <configfile name="user_settings_mkfg"><![CDATA[
/LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
/config/default = "false"
/libs/temp_cache = "."
/tools/prefetch/download_to_cache = "false"
            ]]></configfile>
        </configfiles>
    </macro>
    <macro name="sanitize_query">
        <sanitizer>

34:e407b9da183a

<macros>
    <token name="@TOOL_VERSION@">3.0.8</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->

        </xrefs>
    </xml>
    <token name="@COPY_CONFIGFILE@"><![CDATA[
        mkdir -p ~/.ncbi &&
        cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
    ]]></token>
    <token name="@SET_ACCESSIONS@"><![CDATA[
        #if $input.input_select == "sra_file":
            acc='${input.sra_file.name}' &&
            ln -s '${input.sra_file}' "\$acc" &&

            <configfile name="user_settings_mkfg"><![CDATA[
/LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
/config/default = "false"
/libs/temp_cache = "."
/tools/prefetch/download_to_cache = "false"
/http/timeout/read = "1000"
/repository/user/main/public/root = "."
/repository/user/ad/public/root = "."
/repository/user/default-path = "."
/repository/user/main/public/root = "."
            ]]></configfile>
        </configfiles>
    </macro>
    <macro name="sanitize_query">
        <sanitizer>