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Add Bowtie2 preset options to Tophat2 wrapper.

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This commit is contained in:
Jeremy Goecks
2012-05-31 11:08:24 -04:00
parent 2b023cc95f
commit 51312405f4
2 changed files with 50 additions and 0 deletions
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tools/ngs_rna/tophat2_wrapper.py
+16
View File
@@ -64,6 +64,12 @@ def __main__():
parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' )
parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' )
# Bowtie2 options.
parser.add_option( '', '--b2-very-fast', action='store_true', dest='b2_very_fast')
parser.add_option( '', '--b2-fast', action='store_true', dest='b2_fast')
parser.add_option( '', '--b2-very-sensitive', action='store_true', dest='b2_very_sensitive')
parser.add_option( '', '--b2-sensitive', action='store_true', dest='b2_sensitive')
# Fusion search options.
parser.add_option( '', '--fusion-search', action='store_true', dest='fusion_search' )
parser.add_option( '', '--fusion-anchor-length', dest='fusion_anchor_length' )
@@ -198,6 +204,16 @@ def __main__():
( int( options.fusion_anchor_length ), int( options.fusion_min_dist ),
int( options.fusion_read_mismatches ), int( options.fusion_multireads ),
int( options.fusion_multipairs ), options.fusion_ignore_chromosomes )
# Bowtie2 options.
if options.b2_very_fast:
opts += ' --b2-very-fast'
if options.b2_fast:
opts += ' --b2-fast'
if options.b2_sensitive:
opts += ' --b2-sensitive'
if options.b2_very_sensitive:
opts += ' --b2-very-sensitive'
cmd = cmd % ( opts, index_path, reads )
tools/ngs_rna/tophat2_wrapper.xml
+34
View File
@@ -105,6 +105,13 @@
--fusion-multipairs $params.fusion_search.multipairs
--fusion-ignore-chromosomes $params.fusion_search.ignore_chromosomes
#end if
#if $params.bowtie2_settings.b2_settings == "Yes":
#if $params.bowtie2_settings.preset.b2_preset == "Yes":
--b2-$params.bowtie2_settings.preset.b2_preset_select
#end if
#end if
#end if
</command>
<inputs>
@@ -257,6 +264,33 @@
<param name="ignore_chromosomes" type="text" value='' label="Ignore some chromosomes such as chrM when detecting fusion break points"/>
</when>
</conditional>
<!-- Bowtie2 settings. -->
<conditional name="bowtie2_settings">
<param name="b2_settings" type="select" label="Set Bowtie2 settings">
<option selected="true" value="No">No</option>
<option value="Yes">Yes</option>
</param>
<when value="No" />
<when value="Yes">
<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="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="very-sensitive">Very sensitive</option>
</param>
</when>
<!-- TODO: -->
<when value="No" />
</conditional>
</when>
</conditional>
</when> <!-- full -->
</conditional> <!-- params -->
</inputs>