# HG changeset patch # User iuc # Date 1592326640 0 # Node ID 3d8071386667a7d1cd9869d0c518ce28a4d97de9 # Parent e20b05db0839aef83b90c05320cc6b7ab9a3b4bd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" diff -r e20b05db0839 -r 3d8071386667 cuff_macros.xml --- a/cuff_macros.xml Sun Feb 19 12:11:27 2017 -0500 +++ b/cuff_macros.xml Tue Jun 16 16:57:20 2020 +0000 @@ -66,20 +66,26 @@ - - - + ## Inputs. - #for $input_file in $inputs: - '${input_file}' - #end for - #for $additional_input in $additional_inputs: - #for $input_file in $additional_input.additional_inputs: - '${input_file}' - #end for + #for $i, $input_file in enumerate($inputs): + 'input_$i' #end for getattr(inputs, "__len__", [].__len__)() >= 2 + + + + 10.1038/nbt.1621 + + + + diff -r e20b05db0839 -r 3d8071386667 cuffdiff_wrapper.xml --- a/cuffdiff_wrapper.xml Sun Feb 19 12:11:27 2017 -0500 +++ b/cuffdiff_wrapper.xml Tue Jun 16 16:57:20 2020 +0000 @@ -1,12 +1,12 @@ find significant changes in transcript expression, splicing, and promoter use - cuff_macros.xml + cuff_macros.xml bioconductor-cummerbund - cuffdiff 2>&1 | head -n 1 + &1 | head -n 1]]> - - + + @@ -398,7 +398,5 @@ --num-frag-assign-draws For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts. --min-reps-for-js-test Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. - - 10.1038/nbt.1621 - + diff -r e20b05db0839 -r 3d8071386667 cummeRbund.R --- a/cummeRbund.R Sun Feb 19 12:11:27 2017 -0500 +++ b/cummeRbund.R Tue Jun 16 16:57:20 2020 +0000 @@ -1,2 +1,2 @@ library("cummeRbund") -cuff <- readCufflinks(dir = ".", dbFile = 'cummeRbund.sqlite') \ No newline at end of file +cuff <- readCufflinks(dir = ".", dbFile = "cummeRbund.sqlite")