details: http://www.bx.psu.edu/hg/galaxy/rev/abfddb44a7ca changeset: 3209:abfddb44a7ca user: Anton Nekrutenko <anton(a)bx.psu.edu&gt; date: Wed Jan 06 11:56:55 2010 -0500 description: Small fixes to solid2fastq diffstat: tools/next_gen_conversion/solid2fastq.py | 1 - tools/next_gen_conversion/solid2fastq.xml | 18 +++++++++--------- 2 files changed, 9 insertions(+), 10 deletions(-) diffs (55 lines): diff -r 3863936b6f3e -r abfddb44a7ca tools/next_gen_conversion/solid2fastq.py --- a/tools/next_gen_conversion/solid2fastq.py Tue Jan 05 16:49:56 2010 -0500 +++ b/tools/next_gen_conversion/solid2fastq.py Wed Jan 06 11:56:55 2010 -0500 @@ -177,7 +177,6 @@ r_out = open ( options.rout, 'w' ) db = tempfile.NamedTemporaryFile() - print db.name try: con = sqlite3.connect(db.name) diff -r 3863936b6f3e -r abfddb44a7ca tools/next_gen_conversion/solid2fastq.xml --- a/tools/next_gen_conversion/solid2fastq.xml Tue Jan 05 16:49:56 2010 -0500 +++ b/tools/next_gen_conversion/solid2fastq.xml Wed Jan 06 11:56:55 2010 -0500 @@ -6,8 +6,8 @@ #end if# </command> <inputs> - <param name="input1" type="data" format="csfasta" label="Select Forward reads"/> - <param name="input2" type="data" format="qualsolid" label="Select Forward qualities"/> + <param name="input1" type="data" format="csfasta" label="Select reads"/> + <param name="input2" type="data" format="qualsolid" label="Select qualities"/> <conditional name="is_run"> <param name="paired" type="select" label="Is this a mate-pair run?"> <option value="no" selected="true">No</option> @@ -26,12 +26,12 @@ <option value="">No</option> </param> <param name="trim_first_base" type="select" label="Trim first base?"> - <option value="-f">Yes</option> - <option value="" selected="true">No</option> + <option value="-f">Yes (BWA)</option> + <option value="" selected="true">No (bowtie)</option> </param> <param name="double_encode" type="select" label="Double encode?"> - <option value="-d">Yes</option> - <option value="" selected="true">No</option> + <option value="-d">Yes (BWA)</option> + <option value="" selected="true">No (bowtie)</option> </param> </inputs> <outputs> @@ -93,9 +93,9 @@ **Mate pairs** -If your data is from a mate-paired run, you will have one additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with &quot;_R3&quot;. -In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generated two output files: one for F3 reads and the other for R3 reads. -The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD runs (several hours). +If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with &quot;_R3&quot;. +In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads. +The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours). ------