Mercurial > repos > devteam > fastx_clipper
changeset 4:397201fefb9e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
| author | iuc |
|---|---|
| date | Wed, 22 Aug 2018 11:03:05 -0400 |
| parents | 410c5d0b638a |
| children | 40200bfa25cd |
| files | fastx_clipper.xml macros.xml |
| diffstat | 2 files changed, 10 insertions(+), 2 deletions(-) [+] |
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--- a/fastx_clipper.xml Tue May 08 12:51:16 2018 -0400 +++ b/fastx_clipper.xml Wed Aug 22 11:03:05 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="cshl_fastx_clipper" name="Clip" version="1.0.2"> +<tool id="cshl_fastx_clipper" name="Clip" version="1.0.3"> <description>adapter sequences</description> <macros> <import>macros.xml</import> @@ -14,6 +14,7 @@ $KEEP_N $DISCARD_OPTIONS @FQQUAL@ +@GZIP@ ]]></command> <inputs>
--- a/macros.xml Tue May 08 12:51:16 2018 -0400 +++ b/macros.xml Wed Aug 22 11:03:05 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>