Mercurial > repos > devteam > fastx_artifacts_filter
changeset 4:d8c0849cd623 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
| author | iuc |
|---|---|
| date | Wed, 22 Aug 2018 11:02:45 -0400 |
| parents | ecfaafccf192 |
| children | 84d56dd32719 |
| files | fastx_artifacts_filter.xml macros.xml |
| diffstat | 2 files changed, 9 insertions(+), 1 deletions(-) [+] |
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--- a/fastx_artifacts_filter.xml Tue May 08 12:50:40 2018 -0400 +++ b/fastx_artifacts_filter.xml Wed Aug 22 11:02:45 2018 -0400 @@ -9,6 +9,7 @@ -v -o '$output' @FQQUAL@ +@GZIP@ ]]></command> <inputs>
--- a/macros.xml Tue May 08 12:50:40 2018 -0400 +++ b/macros.xml Wed Aug 22 11:02:45 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>