| Previous changeset 3:43a7370aa010 (2018-05-08) Next changeset 5:ce9cd02d5b88 (2020-01-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a |
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modified:
fastq_quality_filter.xml macros.xml |
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| diff -r 43a7370aa010 -r 7b4468117008 fastq_quality_filter.xml --- 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 |
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| @@ -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> |
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| diff -r 43a7370aa010 -r 7b4468117008 macros.xml --- a/macros.xml Tue May 08 13:26:35 2018 -0400 +++ b/macros.xml Wed Aug 22 11:04:33 2018 -0400 |
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| @@ -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> |