Mercurial > repos > devteam > fastx_trimmer
changeset 4:b98f3fa516a3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
| author | iuc |
|---|---|
| date | Fri, 17 Aug 2018 05:06:06 -0400 |
| parents | bbb007a39ac2 |
| children | 547e8d00f11c |
| files | fastx_trimmer.xml macros.xml test-data/fastx_trimmer2.fastq.gz test-data/fastx_trimmer2.out.gz |
| diffstat | 4 files changed, 14 insertions(+), 2 deletions(-) [+] |
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--- a/fastx_trimmer.xml Tue May 08 13:28:34 2018 -0400 +++ b/fastx_trimmer.xml Fri Aug 17 05:06:06 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="cshl_fastx_trimmer" version="1.0.1" name="Trim sequences"> +<tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences"> <description></description> <macros> <import>macros.xml</import> @@ -10,6 +10,11 @@ -l $last -o '$output' @FQQUAL@ + +#if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): + -z +#end if + ]]></command> <inputs> <expand macro="fastx_input" /> @@ -34,6 +39,13 @@ <param name="last" value="27"/> <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" /> </test> + <test> + <!-- Trim a FASTQ.gz file and output FASTQ.gz --> + <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/> + <param name="first" value="1"/> + <param name="last" value="27"/> + <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" /> + </test> </tests> <help><![CDATA[ **What it does**
--- a/macros.xml Tue May 08 13:28:34 2018 -0400 +++ b/macros.xml Fri Aug 17 05:06:06 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: