Mercurial > repos > geert-vandeweyer > cufflinks
changeset 7:e87fb5178f4b draft
correction to conditional variables
| author | geert-vandeweyer |
|---|---|
| date | Fri, 01 Aug 2014 09:08:07 -0400 |
| parents | 82f0d5660884 |
| children | 065e8d11a08c |
| files | cufflinks_wrapper.xml |
| diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/cufflinks_wrapper.xml Fri Aug 01 08:58:06 2014 -0400 +++ b/cufflinks_wrapper.xml Fri Aug 01 09:08:07 2014 -0400 @@ -18,13 +18,13 @@ ## Include reference annotation? #if $reference_annotation.use_ref == "Use reference annotation": -G $reference_annotation.reference_annotation_file - $compatible_hits_norm + $reference_annoation.compatible_hits_norm #end if #if $reference_annotation.use_ref == "Use reference annotation guide": -g $reference_annotation.reference_annotation_guide_file - --3-overhang-tolerance=$3_overhang_tolerance - --intron-overhang-tolerance=$intron_overhang_tolerance - $no_faux_reads + --3-overhang-tolerance=$reference_annotation.3_overhang_tolerance + --intron-overhang-tolerance=$reference_annotation.intron_overhang_tolerance + $reference_annotation.no_faux_reads #end if ## Bias correction? @@ -189,7 +189,7 @@ <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/> <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/> - <data format="gtf" name="skipped.gtf" lable="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="genes.fpkm_tracking"/> + <data format="gtf" name="skipped.gtf" label="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="genes.fpkm_tracking"/> </outputs> <trackster_conf>