Mercurial > repos > nilesh > sickle
changeset 6:c6a790326d1e
moved from test
author | nilesh |
---|---|
date | Mon, 15 Jul 2013 12:12:41 -0500 |
parents | 4f6349319c0a |
children | dd2ec1b37e96 |
files | sickle.xml tool_dependencies.xml |
diffstat | 2 files changed, 17 insertions(+), 20 deletions(-) [+] |
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--- a/sickle.xml Fri Jul 12 14:01:18 2013 -0500 +++ b/sickle.xml Mon Jul 15 12:12:41 2013 -0500 @@ -1,7 +1,6 @@ <tool id="sickle" name="Sickle"> <description>Windowed Adaptive Trimming of FastQ data</description> <requirements> - <requirement type="package" version="1.2.8">zlib</requirement> <requirement type="package" version="1.21.0">sickle</requirement> </requirements> <command> @@ -84,7 +83,20 @@ <filter>(readtype['single_or_paired'] == 'pe')</filter> </data> </outputs> - + <tests> + <param name="single_or_paired" value="pe"/> + <param name="input_paired1" value="test.f.fastq"/> + <param name="input_paired2" value="test.r.fastq"/> + <param name="qual_type" value="illumina"/> + <param name="qual_threshold" value="20"/> + <param name="length_threshold" value="20"/> + <param name="no_five_prime" value="false"/> + <param name="discard_n" value="false"/> + <output name="output_paired1" value="output.f.fastq"/> + <output name="output_paired2" value="output.r.fastq"/> + <output name="output_paired_single" value="output.fastq"/> + </tests> + <help> Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end and some towards the 5'-end as well. Incorrectly called bases in both regions negatively impact assembles, mapping, and downstream bioinformatics analyses.
--- a/tool_dependencies.xml Fri Jul 12 14:01:18 2013 -0500 +++ b/tool_dependencies.xml Mon Jul 15 12:12:41 2013 -0500 @@ -1,31 +1,16 @@ <?xml version="1.0"?> <tool_dependency> - <package name="zlib" version="1.2.8"> + <package name="sickle" version="1.21.0"> <install version="1.0"> <actions> <action type="download_by_url">http://zlib.net/zlib-1.2.8.tar.gz</action> <action type="shell_command">./configure --prefix=$INSTALL_DIR/zlib</action> <action type="shell_command">make</action> <action type="shell_command">make install prefix=$INSTALL_DIR/zlib</action> - <action type="set_environment"> - <environment_variable name="ZLIB_PATH" action="set_to">$INSTALL_DIR/zlib/lib</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/zlib/lib</environment_variable> - </action> - </actions> - </install> - <readme> - zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms. - </readme> - </package> - <package name="sickle" version="1.21.0"> - <install version="1.0"> - <actions> <action type="shell_command">git clone https://github.com/najoshi/sickle.git</action> - <action type="shell_command">make LIBS="-L$ENV[ZLIB_PATH] -lz"</action> + <action type="shell_command">cd ./sickle && make LIBS="-L$INSTALL_DIR/zlib/lib -lz"</action> <action type="move_file"> - <source>sickle</source> + <source>sickle/sickle</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment">