comparison fastq_dump.xml @ 5:6f68b86da01a draft default tip

planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty

4:b9408bf2a9ac

<tool id="fastq_dump" name="Extract reads" version="1.2.4">
    <description>in FASTQ/A format from NCBI SRA.</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
        <![CDATA[
    ## 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;
    #if $input.input_select == "file":
        fastq-dump --log-level fatal --accession '${input.file.name}'
    #else:

5:6f68b86da01a

<tool id="fastq_dump" name="Extract reads" version="1.2.5">
    <description>in FASTQ/A format from NCBI SRA.</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
        <![CDATA[
    ## Need to set the home directory to the current working directory,
    ## else the tool tries to write to home/.ncbi and fails when used 
    ## within production environments. 
    export HOME=\$PWD;
    vdb-config --restore-defaults;
    #if $input.input_select == "file":
        fastq-dump --log-level fatal --accession '${input.file.name}'
    #else: