2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc97d0a852cb/ changeset: dc97d0a852cb user: jgoecks date: 2011-06-07 20:31:35 summary: Rename and reorder Cuffdiff outputs for clarity. affected #: 1 file (172 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.xml Tue Jun 07 11:32:11 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Tue Jun 07 14:31:35 2011 -0400 @@ -132,17 +132,17 @@ </inputs><outputs> - <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: isoform expression"/> - <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene expression"/> - <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups expression"/> - <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> - <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> + <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing"/> + <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing"/> + <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing"/> + <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing"/> + <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> + <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing"/> + <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> + <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing"/><data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> - <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> - <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> - <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> - <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> - <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> + <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing"/> + <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking"/></outputs><tests> @@ -164,17 +164,17 @@ Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? --> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/> - <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> - <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> - <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/> - <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> - <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> - <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/><output name="splicing_diff" file="cuffdiff_out9.txt"/><output name="promoters_diff" file="cuffdiff_out10.txt"/><output name="cds_diff" file="cuffdiff_out11.txt"/> + <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> + <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> + <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> + <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/></test></tests> http://bitbucket.org/galaxy/galaxy-central/changeset/801a4a2a5921/ changeset: 801a4a2a5921 user: jgoecks date: 2011-06-07 20:31:58 summary: Merge. affected #: 1 file (105 bytes) --- a/templates/library/common/ldda_info.mako Tue Jun 07 14:31:35 2011 -0400 +++ b/templates/library/common/ldda_info.mako Tue Jun 07 14:31:58 2011 -0400 @@ -136,20 +136,22 @@ <div>${ldda.blurb}</div></div> %for name, spec in ldda.metadata.spec.items(): - <div class="form-row"> - <label>${spec.desc.replace( ' (click box & select)', '' )}:</label> - <% - metadata_val = ldda.metadata.get( name ) - if isinstance( metadata_val, trans.model.MetadataFile ): - metadata_val = metadata_val.file_name - elif isinstance( metadata_val, list ): - # Make sure list items are strings - metadata_val = [ str( item ) for item in metadata_val ] - metadata_val = ', '.join( metadata_val ) - %> - ${metadata_val} - <div style="clear: both"></div> - </div> + %if spec.visible: + <div class="form-row"> + <label>${spec.desc.replace( ' (click box & select)', '' )}:</label> + <% + metadata_val = ldda.metadata.get( name ) + if isinstance( metadata_val, trans.model.MetadataFile ): + metadata_val = metadata_val.file_name + elif isinstance( metadata_val, list ): + # Make sure list items are strings + metadata_val = [ str( item ) for item in metadata_val ] + metadata_val = ', '.join( metadata_val ) + %> + ${metadata_val} + <div style="clear: both"></div> + </div> + %endif %endfor %if ldda.peek != "no peek": <div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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