Mercurial > repos > galaxyp > pepquery2_index

comparison macros.xml @ 2:c56ca72c129e draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f
author galaxyp
date Wed, 08 May 2024 17:12:28 +0000
parents 0f0095bde898
children
comparison
equal deleted inserted replaced
1:0f0095bde898 2:c56ca72c129e
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.0.2</token> 2 <token name="@TOOL_VERSION@">2.0.2</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">2</token>
4 <xml name="citations"> 4 <xml name="citations">
5 <citations> 5 <citations>
6 <citation type="doi">10.1101/gr.235028.118</citation> 6 <citation type="doi">10.1101/gr.235028.118</citation>
7 <citation type="doi">10.1038/s41467-020-15456-w</citation> 7 <citation type="doi">10.1038/s41467-020-15456-w</citation>
8 </citations> 8 </citations>
18 #else 18 #else
19 #return $input1.name 19 #return $input1.name
20 #end if 20 #end if
21 #end def 21 #end def
22 #def clean($name1) 22 #def clean($name1)
23 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) 23 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
24 #return $name_clean 24 #return $name_clean
25 #end def 25 #end def
26 #def ln_name($ds) 26 #def ln_name($ds)
27 #set $ext = '' 27 #set $ext = ''
28 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') 28 #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
29 #set $ext = ".mzML" 29 #set $ext = ".mzML"
30 #else if $ds.is_of_type('mzxml') 30 #else if $ds.is_of_type('mzxml')
31 #set $ext = ".mzXML" 31 #set $ext = ".mzXML"
32 #else if $ds.is_of_type('mgf') 32 #else if $ds.is_of_type('mgf')
33 #set $ext = ".mgf" 33 #set $ext = ".mgf"
34 #else if $ds.is_of_type('thermo.raw')
35 #set $ext = ".raw"
36 #else if $ds.is_of_type('fasta') 34 #else if $ds.is_of_type('fasta')
37 #set $ext = ".fasta" 35 #set $ext = ".fasta"
38 #end if 36 #end if
39 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) 37 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
40 #return $name 38 #return $name