Mercurial > repos > jjohnson > encyclopedia_prosit_csv_to_library
changeset 4:602d01de42b4 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
| author | jjohnson |
|---|---|
| date | Tue, 07 Jul 2020 11:56:02 -0400 |
| parents | 7d58a052411a |
| children | bd7ce1544554 |
| files | encyclopedia_prosit_csv_to_library.xml macros.xml |
| diffstat | 2 files changed, 3 insertions(+), 5 deletions(-) [+] |
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--- a/encyclopedia_prosit_csv_to_library.xml Thu Jul 02 11:07:21 2020 -0400 +++ b/encyclopedia_prosit_csv_to_library.xml Tue Jul 07 11:56:02 2020 -0400 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ EncyclopeDIA -convert -prositcsvtolibrary -i '$i' -f '$f'
--- a/macros.xml Thu Jul 02 11:07:21 2020 -0400 +++ b/macros.xml Tue Jul 07 11:56:02 2020 -0400 @@ -31,14 +31,12 @@ #end if #end def #def clean($name1) - ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz')))) - ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz'))) - #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) #return $name_clean #end def #def ln_name($ds) #set $ext = '' - #if $ds.is_of_type('mzml') + #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') #set $ext = ".mzML" #else if $ds.is_of_type('elib') #set $ext = ".elib"