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Small fixes to solid2fastq

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Anton Nekrutenko
2010-01-06 11:56:55 -05:00
parent f9d123fb82
commit 9d6a9ee9b2
2 changed files with 9 additions and 10 deletions
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tools/next_gen_conversion/solid2fastq.py
-1
View File
@@ -177,7 +177,6 @@ def main():
r_out = open ( options.rout, 'w' )
db = tempfile.NamedTemporaryFile()
print db.name
try:
con = sqlite3.connect(db.name)
tools/next_gen_conversion/solid2fastq.xml
+9 -9
View File
@@ -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 @@ Quality scores::
**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).
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