comparison sam_dump.xml @ 16:aad3885b3216 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"

15:f5ea3ce9b9b0

<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.4">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>sam-dump --version</version_command>
    <command detect_errors="exit_code">
<![CDATA[
        @SET_ACCESSIONS@

        ## Need to set the home directory to the current working directory,
        ## else the tool tries to write to home/.ncbi and fails when used
        ## with a cluster manager.
        export HOME=\$PWD &&
        vdb-config --restore-defaults &&
        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.

        #if $input.input_select == "file":
            sam-dump --log-level fatal  '${input.file.name}'
        #else:
            #if ( str( $adv.region ) == "" ):
                ASCP_PATH=`command -v ascp` &&
                ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
                prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
                ## Duplicate vdb-config, in case settings changed between prefetch and
                ## dump command.
                vdb-config -s "/repository/user/main/public/root=\$PWD" &&
            #end if
            sam-dump --log-level fatal --disable-multithreading

16:aad3885b3216

<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.10">samtools</requirement>
    </expand>
    <version_command>sam-dump --version</version_command>
    <command detect_errors="exit_code">
<![CDATA[
        @SET_ACCESSIONS@

        ## Need to set the home directory to the current working directory,
        ## else the tool tries to write to home/.ncbi and fails when used
        ## with a cluster manager.
        @CONFIGURE_TIMEOUT@
        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.

        #if $input.input_select == "file":
            sam-dump --log-level fatal  '${input.file.name}'
        #else:
            #if ( str( $adv.region ) == "" ):
                prefetch -X 200000000 "\$acc" &&
                ## Duplicate vdb-config, in case settings changed between prefetch and
                ## dump command.
                vdb-config -s "/repository/user/main/public/root=\$PWD" &&
            #end if
            sam-dump --log-level fatal --disable-multithreading