# HG changeset patch # User iuc # Date 1594059576 0 # Node ID 5e3670f9401920fb4e2e1bd8efa1e92c88221bf3 # Parent dc97f71022e5a8ae6faa011ae7db16e7958f6a15 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit 6b66cbbde16c35593fe95066ea2b91623bf35140" diff -r dc97f71022e5 -r 5e3670f94019 cuff_macros.xml --- a/cuff_macros.xml Tue Jun 16 16:58:39 2020 +0000 +++ b/cuff_macros.xml Mon Jul 06 18:19:36 2020 +0000 @@ -1,91 +1,95 @@ - 2.2.1 + 2.2.1 + + + + cufflinks + + + - - - cufflinks - - - + + + + + value and "," not in value + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #if $in_type.set_in_type in ['BAM', 'CXB'] - #for $condition in $in_type.conditions: - #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) - '$samples' - #end for - #elif $in_type.set_in_type == 'CONDITION_LIST' - #for $sample in $in_type.conditions: - '$sample' - #end for - #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' - #for $condition_list in $in_type.conditions: - #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) - '$samples' - #end for - #end if - - - #import re - #if $in_type.set_in_type in ['BAM', 'CXB'] - #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' - #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] - #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' - #end if - --labels $labels - - - - - - - ## Inputs. - #for $i, $input_file in enumerate($inputs): - 'input_$i' - #end for - - getattr(inputs, "__len__", [].__len__)() >= 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + getattr(inputs, "__len__", [].__len__)() >= 2 - - - 10.1038/nbt.1621 - - - + + + 10.1038/nbt.1621 + + + diff -r dc97f71022e5 -r 5e3670f94019 cuffnorm_wrapper.xml --- a/cuffnorm_wrapper.xml Tue Jun 16 16:58:39 2020 +0000 +++ b/cuffnorm_wrapper.xml Mon Jul 06 18:19:36 2020 +0000 @@ -1,4 +1,4 @@ - + Create normalized expression levels cuff_macros.xml @@ -210,7 +210,7 @@ **Input format** -Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. +Cuffnorm takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. ------ @@ -223,15 +223,9 @@ ------- -**Settings** - -All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. +**Parameter list** ------- - -**Cuffdiff parameter list** - -This is a list of implemented Cuffdiff options:: +This is a list of implemented Cuffnorm options:: --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags