1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/8cbdb2d339fe/ changeset: 8cbdb2d339fe user: jgoecks date: 2012-06-06 21:27:59 summary: Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper. affected #: 3 files

diff -r 3db661b25774e2cb3eba6c156220f181eb28cb95 -r 8cbdb2d339feb017e72ca73915e090c0aa7d07e1 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -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>

diff -r 3db661b25774e2cb3eba6c156220f181eb28cb95 -r 8cbdb2d339feb017e72ca73915e090c0aa7d07e1 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -19,9 +19,12 @@ 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 @@ 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 )

diff -r 3db661b25774e2cb3eba6c156220f181eb28cb95 -r 8cbdb2d339feb017e72ca73915e090c0aa7d07e1 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -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>

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

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