details: http://www.bx.psu.edu/hg/galaxy/rev/e59720d5c6b8 changeset: 3797:e59720d5c6b8 user: rc date: Thu May 20 15:36:07 2010 -0400 description: added more options to the sff converter tool
diffstat:
tools/filters/sff_extractor.xml | 27 ++++++++++++++++++++++----- 1 files changed, 22 insertions(+), 5 deletions(-)
diffs (39 lines):
diff -r 218cfbba30ce -r e59720d5c6b8 tools/filters/sff_extractor.xml --- a/tools/filters/sff_extractor.xml Thu May 20 14:16:08 2010 -0400 +++ b/tools/filters/sff_extractor.xml Thu May 20 15:36:07 2010 -0400 @@ -1,13 +1,30 @@ <tool id="Sff_extractor" name="SFF converter" version="1.0.0"> <description></description> - <command interpreter="python">sff_extract.py -s $out_file1 -q $out_file2 -x $out_file3 $input</command> - <inputs> + <command interpreter="python"> + #if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input + #elif str($fastq_output) == "fastq_true" #sff_extract.py $clip --fastq --seq_file=$out_file1 --xml_file=$out_file2 $input + #end if# + </command> + <inputs> <param format="sff" name="input" type="data" label="Extract from this dataset"/> + <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence"> + <option value="">No</option> + <option value="--clip">Yes</option> + </param> + <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" /> </inputs> <outputs> - <data format="fasta" name="out_file1" /> - <data format="qual" name="out_file2" /> - <data format="xml" name="out_file3" /> + <data format="fastq" name="out_file1" > + <filter>fastq_output is True</filter> + </data> + <data format="xml" name="out_file2"> + </data> + <data format="fasta" name="out_file3"> + <filter>fastq_output is False</filter> + </data> + <data format="qual" name="out_file4"> + <filter>fastq_output is False</filter> + </data> </outputs> <help> **What it does**