1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4368df9df278/ changeset: 4368df9df278 user: jgoecks date: 2012-09-13 22:04:03 summary: Fix bug in tool_form JS reorganization and fix labels for two Cuffdiff options. affected #: 2 files diff -r a683489600be0deb53e5abe6eb07c399e417342e -r 4368df9df27896599a64236a6f8f80ebb0baf8c5 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -12,6 +12,7 @@ </%def><%def name="javascripts()"> + ${parent.javascripts()} ${h.js( "galaxy.panels", "libs/jquery/jquery.autocomplete", "libs/jquery/jstorage" )} <script type="text/javascript"> $(function() { diff -r a683489600be0deb53e5abe6eb07c399e417342e -r 4368df9df27896599a64236a6f8f80ebb0baf8c5 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -24,8 +24,8 @@ ## Set paired-end data parameters? #if $singlePaired.sPaired == "Yes": - -m $singlePaired.mean_inner_distance - -s $singlePaired.inner_distance_std_dev + -m $singlePaired.frag_mean_len + -s $singlePaired.frag_len_std_dev #end if ## Normalization? @@ -120,8 +120,8 @@ </param><when value="No"></when><when value="Yes"> - <param name="mean_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs"/> - <param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/> + <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"/></when></conditional></inputs> @@ -226,8 +226,8 @@ This is a list of implemented Cuffdiff options:: - -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. - -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. + -m INT Average fragement length; default 200 + -s INT Fragment legnth standard deviation; default 80 -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 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.