1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8b7dfceabe3e/ changeset: 8b7dfceabe3e user: jgoecks date: 2012-09-24 01:34:11 summary: Fix Cuffdiff parameter group naming. affected #: 1 file diff -r 3574c1fa4cb3494f82fd1915c63da6154b230756 -r 8b7dfceabe3ea6cc15001f05a623157e95f1bcb7 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -22,11 +22,11 @@ --cds_diff_output=$cds_diff --promoters_diff_output=$promoters_diff - ## Set paired-end data parameters? - #if $singlePaired.sPaired == "Yes": - -m $singlePaired.frag_mean_len - -s $singlePaired.frag_len_std_dev - #end if + ## Set advanced data parameters? + #if $additional.sAdditional == "Yes": + -m $additional.frag_mean_len + -s $additional.frag_len_std_dev + #end if ## Normalization? #if str($do_normalization) == "Yes": @@ -113,15 +113,15 @@ </when><when value="No"></when></conditional> - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Set Parameters for Paired-end Reads? (not recommended)"> + <conditional name="additional"> + <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)"><option value="No">No</option><option value="Yes">Yes</option></param><when value="No"></when><when value="Yes"> - <param name="frag_mean_len" type="integer" value="20" label="Average Fragment Length"/> - <param name="frag_len_std_dev" type="integer" value="20" label="Fragment Length Standard Deviation"/> + <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/> + <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/></when></conditional></inputs> @@ -154,7 +154,7 @@ <param name="min_alignment_count" value="0" /><param name="do_bias_correction" value="No" /><param name="do_normalization" value="No" /> - <param name="sPaired" value="single"/> + <param name="sAdditional" value="No"/><!-- Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? 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.