Mercurial > repos > devteam > fastq_quality_filter
changeset 4:7b4468117008 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
| author | iuc |
|---|---|
| date | Wed, 22 Aug 2018 11:04:33 -0400 |
| parents | 43a7370aa010 |
| children | ce9cd02d5b88 |
| files | fastq_quality_filter.xml macros.xml |
| diffstat | 2 files changed, 10 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/fastq_quality_filter.xml Tue May 08 13:26:35 2018 -0400 +++ b/fastq_quality_filter.xml Wed Aug 22 11:04:33 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="cshl_fastq_quality_filter" version="1.0.1" name="Filter by quality"> +<tool id="cshl_fastq_quality_filter" version="1.0.2" name="Filter by quality"> <description></description> <macros> <import>macros.xml</import> @@ -11,6 +11,7 @@ -v -o '$output' @FQQUAL@ +@GZIP@ ]]></command> <inputs>
--- a/macros.xml Tue May 08 13:26:35 2018 -0400 +++ b/macros.xml Wed Aug 22 11:04:33 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>