comparison macros.xml @ 2:c32806a80862 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f

1:b5489f81c2fa

 <macros>
    <token name="@TOOL_VERSION@">2.0.2</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.235028.118</citation>
            <citation type="doi">10.1038/s41467-020-15456-w</citation>
        </citations>

    #else
        #return $input1.name
    #end if
#end def
#def clean($name1)
    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
    #return $name_clean
#end def
#def ln_name($ds)
    #set $ext = ''
    #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
        #set $ext = ".mzML"
    #else if $ds.is_of_type('mzxml')
        #set $ext = ".mzXML"
    #else if $ds.is_of_type('mgf')
        #set $ext = ".mgf"
    #else if $ds.is_of_type('thermo.raw')
        #set $ext = ".raw"
    #else if $ds.is_of_type('fasta')
        #set $ext = ".fasta"
    #end if
    #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
    #return $name

2:c32806a80862

 <macros>
    <token name="@TOOL_VERSION@">2.0.2</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.235028.118</citation>
            <citation type="doi">10.1038/s41467-020-15456-w</citation>
        </citations>

    #else
        #return $input1.name
    #end if
#end def
#def clean($name1)
    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
    #return $name_clean
#end def
#def ln_name($ds)
    #set $ext = ''
    #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
        #set $ext = ".mzML"
    #else if $ds.is_of_type('mzxml')
        #set $ext = ".mzXML"
    #else if $ds.is_of_type('mgf')
        #set $ext = ".mgf"
    #else if $ds.is_of_type('fasta')
        #set $ext = ".fasta"
    #end if
    #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
    #return $name