details:
http://www.bx.psu.edu/hg/galaxy/rev/abfddb44a7ca
changeset: 3209:abfddb44a7ca
user: Anton Nekrutenko <anton(a)bx.psu.edu>
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 "_R3".
-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 "_R3".
+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).
------