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Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper.

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This commit is contained in:
Jeremy Goecks
2012-06-06 15:27:59 -04:00
parent a8a3c23941
commit 63fec8c332
3 changed files with 36 additions and 4 deletions
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tools/ngs_rna/tophat2_wrapper.xml
+2 -2
View File
@@ -281,8 +281,8 @@
<when value="Yes">
<param name="b2_preset_select" type="select" label="Preset option">
<option value="very-fast">Very fast</option>
<option selected="true" value="fast">Fast</option>
<option value="sensitive">Sensitive</option>
<option value="fast">Fast</option>
<option selected="true" value="sensitive">Sensitive</option>
<option value="very-sensitive">Very sensitive</option>
</param>
</when>
tools/sr_mapping/bowtie2_wrapper.py
+8 -2
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@@ -19,9 +19,12 @@ def __main__():
parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
parser.add_option( '', '--single-paired', dest='single_paired', help='' )
parser.add_option( '', '--settings', dest='settings', help='' )
parser.add_option( '', '--end-to-end', dest='end_to_end', action="store_true" )
parser.add_option( '', '--local', dest='local', action="store_true" )
parser.add_option( '', '--preset-alignment', dest='preset_alignment')
(options, args) = parser.parse_args()
# Creat bowtie index if necessary.
tmp_index_dir = tempfile.mkdtemp()
if options.own_file:
@@ -73,7 +76,10 @@ def __main__():
if options.settings == 'preSet':
pass
else:
pass
if options.local:
opts += ' --local'
if options.preset_alignment:
opts += " --" + options.preset_alignment
# Final command:
cmd = cmd % ( opts, index_path, reads, options.output )
tools/sr_mapping/bowtie2_wrapper.xml
+26
View File
@@ -34,6 +34,12 @@
## Set params.
--settings=$params.settingsType
#if str($params.align_type) == "end_to_end":
--end-to-end --preset-alignment=$params.preset.align_preset_select
#else:
--local --preset-alignment=$params.preset.align_preset_select-local
#end if
</command>
<inputs>
<conditional name="singlePaired">
@@ -75,6 +81,26 @@
<when value="preSet" />
<!-- Full/advanced params. -->
<when value="full">
<param name="align_type" type="select" label="Type of alignment">
<option selected="true" value="end_to_end">End to end</option>
<option value="local">Local</option>
</param>
<conditional name="preset">
<param name="b2_preset" type="select" label="Use Preset options">
<option selected="true" value="Yes">Yes</option>
<option value="No">No</option>
</param>
<when value="Yes">
<param name="align_preset_select" type="select" label="Preset option">
<option value="very-fast">Very fast</option>
<option value="fast">Fast</option>
<option selected="true" value="sensitive">Sensitive</option>
<option value="very-sensitive">Very sensitive</option>
</param>
</when>
<!-- TODO: -->
<when value="No" />
</conditional>
</when> <!-- full -->
</conditional> <!-- params -->
</inputs>