Mercurial > repos > devteam > fastq_to_fasta
changeset 3:4498e994e31b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
| author | iuc |
|---|---|
| date | Wed, 22 Aug 2018 11:02:27 -0400 |
| parents | 44ed3f74ea7a |
| children | 5dbca5fbdc45 |
| files | fastq_to_fasta.xml macros.xml |
| diffstat | 2 files changed, 10 insertions(+), 2 deletions(-) [+] |
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--- a/fastq_to_fasta.xml Tue May 08 12:50:22 2018 -0400 +++ b/fastq_to_fasta.xml Wed Aug 22 11:02:27 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.1"> +<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2"> <description>converter from FASTX-toolkit</description> <macros> <import>macros.xml</import> @@ -10,6 +10,7 @@ $RENAMESEQ -o '$output' -v @FQQUAL@ +@GZIP@ ]]></command> <inputs> <expand macro="fastq_input" />
--- a/macros.xml Tue May 08 12:50:22 2018 -0400 +++ b/macros.xml Wed Aug 22 11:02:27 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>