Mercurial > repos > devteam > fastx_renamer
changeset 3:3599f5451ee2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
| author | iuc |
|---|---|
| date | Wed, 22 Aug 2018 11:05:29 -0400 |
| parents | d8a3d31554d7 |
| children | b29d37ca9e41 |
| files | fastx_renamer.xml macros.xml |
| diffstat | 2 files changed, 9 insertions(+), 1 deletions(-) [+] |
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--- a/fastx_renamer.xml Tue May 08 13:28:10 2018 -0400 +++ b/fastx_renamer.xml Wed Aug 22 11:05:29 2018 -0400 @@ -10,6 +10,7 @@ -o '$output' -v @FQQUAL@ +@GZIP@ ]]></command> <inputs>
--- a/macros.xml Tue May 08 13:28:10 2018 -0400 +++ b/macros.xml Wed Aug 22 11:05:29 2018 -0400 @@ -2,7 +2,7 @@ <macros> <token name="@CATS@"> #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): - zcat -f '$input' | + gunzip -c -f '$input' | #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): bzcat -f '$input' | #else: @@ -18,6 +18,13 @@ #end if ]]> </token> + <token name="@GZIP@"> + <![CDATA[ + #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): + -z + #end if + ]]> + </token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>