1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/9ae91fb49fdd/ changeset: 9ae91fb49fdd user: jgoecks date: 2012-05-31 17:08:24 summary: Add Bowtie2 preset options to Tophat2 wrapper. affected #: 2 files

diff -r 2f971a75d8575082685e97325967fedc67b462a4 -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -64,6 +64,12 @@ 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 @@ ( 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 )

diff -r 2f971a75d8575082685e97325967fedc67b462a4 -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -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>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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