1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/143f7f55098a/ Changeset: 143f7f55098a User: jgoecks Date: 2013-08-01 20:51:06 Summary: Cuffdiff wrapper: add option to output read group datasets. Affected #: 1 file diff -r 6e36021502522213aca87e0b49f0bf0384eddfa1 -r 143f7f55098ae936481e5fcb1be85a3e5b5f159b tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -96,8 +96,13 @@ <when value="No"></when></conditional> + <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <conditional name="additional"> - <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)"> + <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)"><option value="No">No</option><option value="Yes">Yes</option></param> @@ -114,6 +119,21 @@ </stdio><outputs> + <!-- Optional read group datasets. --> + <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" > + <filter>(params['include_read_group_files'] == 'Yes'</filter> + </data> + <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" > + <filter>(params['include_read_group_files'] == 'Yes'</filter> + </data> + <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" > + <filter>(params['include_read_group_files'] == 'Yes'</filter> + </data> + <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" > + <filter>(params['include_read_group_files'] == 'Yes'</filter> + </data> + + <!-- Standard datasets. --><data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" /><data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" /><data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.