# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks jeremy.goecks@emory.edu # Date 1288979059 14400 # Node ID 11abfc8eed60c0bdd231d06992f72001a2c785fa # Parent 9545e8675a5d43408d75c66fcf3115cbdaf4af8a Update cufflinks and cuffdiff wrappers to indicate that, as of version 0.9, setting parameters for paired-end reads is not recommended.

--- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -25,6 +25,11 @@ --inputA=$gtf_input --input1=$aligned_reads1 --input2=$aligned_reads2 + + #if $singlePaired.sPaired == "Yes": + -m $singlePaired.mean_inner_distance + -s $singlePaired.inner_distance_std_dev + #end if </command><inputs><param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/> @@ -34,12 +39,12 @@ <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/><param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> + <param name="sPaired" type="select" label="Set Parameters for Paired-end Reads? (not recommended)"> + <option value="No">No</option> + <option value="Yes">Yes</option></param> - <when value="single"></when> - <when value="paired"> + <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"/></when>

--- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -17,7 +17,7 @@ #if $reference_annotation.use_ref == "Yes": -G $reference_annotation.reference_annotation_file #end if - #if $singlePaired.sPaired == "paired": + #if $singlePaired.sPaired == "Yes": -m $singlePaired.mean_inner_distance -s $singlePaired.inner_distance_std_dev #end if @@ -39,12 +39,12 @@ </when></conditional><conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> + <param name="sPaired" type="select" label="Set Parameters for Paired-end Reads? (not recommended)"> + <option value="No">No</option> + <option value="Yes">Yes</option></param> - <when value="single"></when> - <when value="paired"> + <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"/></when>