comparison encyclopedia_library_to_blib.xml @ 1:7603f590a1a1 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"

0:d37d900794f6

    <description>Convert EncyclopeDIA Library to BLIB for Skyline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        EncyclopeDIA -convert -libtoblib
        -i '$i'
        -o '$output'
        #if $istest == 'yes'
        && sqlite3 -readonly '$output' 'SELECT distinct peptideSeq FROM RefSpectra;' > '$test_output'
        #end if

1:7603f590a1a1

    <description>Convert EncyclopeDIA Library to BLIB for Skyline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        EncyclopeDIA -convert -libtoblib
            -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
            -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
            -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
        -i '$i'
        -o '$output'
        #if $istest == 'yes'
        && sqlite3 -readonly '$output' 'SELECT distinct peptideSeq FROM RefSpectra;' > '$test_output'
        #end if