Mercurial > repos > devteam > fastx_trimmer
changeset 6:61b4cedc8934 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
| author | iuc |
|---|---|
| date | Thu, 30 Jan 2020 13:31:32 -0500 |
| parents | 547e8d00f11c |
| children | 73194cdd4f57 |
| files | fastx_trimmer.xml macros.xml test-data/fastx_trimmer2.fastq.bz2 test-data/fastx_trimmer2.out.bz2 test-data/fastx_trimmer2.out.gz |
| diffstat | 5 files changed, 16 insertions(+), 5 deletions(-) [+] |
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--- a/fastx_trimmer.xml Wed Aug 22 11:06:02 2018 -0400 +++ b/fastx_trimmer.xml Thu Jan 30 13:31:32 2020 -0500 @@ -1,16 +1,18 @@ -<tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences"> +<tool id="cshl_fastx_trimmer" version="1.0.2+galaxy0" name="Trim sequences"> <description></description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="1.0.8">bzip2</requirement> + </expand> <command detect_errors="exit_code"><![CDATA[ @CATS@ fastx_trimmer -v -f $first -l $last --o '$output' @FQQUAL@ @GZIP@ +> '$output' ]]></command> <inputs> <expand macro="fastx_input" /> @@ -36,12 +38,19 @@ <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" /> </test> <test> - <!-- Trim a FASTQ.gz file and output FASTQ.gz --> + <!-- 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> + <test> + <!-- Trim a FASTQ.bz2 file and output FASTQ.bz2 --> + <param name="input" value="fastx_trimmer2.fastq.bz2" ftype="fastqsanger.bz2"/> + <param name="first" value="1"/> + <param name="last" value="27"/> + <output name="output" ftype="fastqsanger.bz2" decompress="true" file="fastx_trimmer2.out.bz2" /> + </test> </tests> <help><![CDATA[ **What it does**
--- a/macros.xml Wed Aug 22 11:06:02 2018 -0400 +++ b/macros.xml Thu Jan 30 13:31:32 2020 -0500 @@ -21,7 +21,9 @@ <token name="@GZIP@"> <![CDATA[ #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): - -z + | gzip -c + #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): + | bzip2 -c #end if ]]> </token>