1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/896846341a36/
changeset: 896846341a36
user: peterjc
date: 2011-08-12 11:33:26
summary: Add missing requirement and fix incorrect help text in extract sequence tool
affected #: 1 file (125 bytes)
--- a/tools/extract/extract_genomic_dna.xml Thu Aug 11 18:37:14 2011 -0400
+++ b/tools/extract/extract_genomic_dna.xml Fri Aug 12 10:33:26 2011 +0100
@@ -1,4 +1,4 @@
-<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1">
+<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.2"><description>using coordinates from assembled/unassembled genomes</description><command interpreter="python">
extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey
@@ -51,6 +51,9 @@
</change_format></data></outputs>
+ <requirements>
+ <requirement type="binary">faToTwoBit</requirement>
+ </requirements><tests><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
@@ -110,7 +113,7 @@
.. class:: warningmark
-This tool requires tabular formatted data. If your data is not TAB delimited, use *Text Manipulation->Convert*.
+This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use *Text Manipulation->Convert*.
.. class:: warningmark
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/0ef81af1de09/
changeset: 0ef81af1de09
user: jgoecks
date: 2011-08-11 16:14:53
summary: Add GTF-guide option to Cufflinks wrapper. Patch from Ilya Chorny.
affected #: 2 files (843 bytes)
--- a/tools/ngs_rna/cufflinks_wrapper.py Thu Aug 11 09:53:14 2011 -0400
+++ b/tools/ngs_rna/cufflinks_wrapper.py Thu Aug 11 10:14:53 2011 -0400
@@ -33,6 +33,7 @@
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.')
parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' )
+ parser.add_option( '-g', '--GTF-guide', dest='GTFguide', help='use reference transcript annotation to guide assembly' )
# Normalization options.
parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" )
@@ -104,6 +105,8 @@
cmd += ( " -m %i" % int ( options.inner_mean_dist ) )
if options.GTF:
cmd += ( " -G %s" % options.GTF )
+ if options.GTFguide:
+ cmd += ( " -g %s" % options.GTFguide )
if options.num_importance_samples:
cmd += ( " --num-importance-samples %i" % int ( options.num_importance_samples ) )
if options.max_mle_iterations:
--- a/tools/ngs_rna/cufflinks_wrapper.xml Thu Aug 11 09:53:14 2011 -0400
+++ b/tools/ngs_rna/cufflinks_wrapper.xml Thu Aug 11 10:14:53 2011 -0400
@@ -14,9 +14,12 @@
-j $pre_mrna_fraction
## Include reference annotation?
- #if $reference_annotation.use_ref == "Yes":
+ #if $reference_annotation.use_ref == "use reference annotation":
-G $reference_annotation.reference_annotation_file
#end if
+ #if $reference_annotation.use_ref == "use reference annotation guide":
+ -g $reference_annotation_guide.reference_annotation_guide_file
+ #end if
## Set paired-end parameters?
#if $singlePaired.sPaired == "Yes":
@@ -53,17 +56,21 @@
<conditional name="reference_annotation"><param name="use_ref" type="select" label="Use Reference Annotation"><option value="No">No</option>
- <option value="Yes">Yes</option>
+ <option value="Use reference annotation">Use reference annotation</option>
+ <option value="Use reference annotation guide">Use reference annotation as guide</option></param><when value="No"></when>
- <when value="Yes">
- <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
- </when>
+ <when value="Use reference annotation">
+ <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+ </when>
+ <when value="Use reference annotation guide">
+ <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/>
+ </when></conditional><conditional name="bias_correction"><param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
- <option value="Yes">Yes</option><option value="No">No</option>
+ <option value="Yes">Yes</option></param><when value="Yes"><conditional name="seq_source">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9/
changeset: 07de40a5a0b9
user: jgoecks
date: 2011-08-11 15:53:14
summary: Remove unspecified build validator from extract_genomic_dna tool because it can work with a custom fasta.
affected #: 1 file (63 bytes)
--- a/tools/extract/extract_genomic_dna.xml Wed Aug 10 16:50:04 2011 -0400
+++ b/tools/extract/extract_genomic_dna.xml Thu Aug 11 09:53:14 2011 -0400
@@ -23,9 +23,7 @@
#end if
</command><inputs>
- <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in">
- <validator type="unspecified_build" />
- </param>
+ <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"/><param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets."><option value="yes">Yes</option><option value="no">No</option>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/431c06394bb1/
changeset: 431c06394bb1
user: jgoecks
date: 2011-08-10 22:50:04
summary: Set Trackster overview height correctly.
affected #: 1 file (5 bytes)
--- a/static/scripts/trackster.js Wed Aug 10 16:42:01 2011 -0400
+++ b/static/scripts/trackster.js Wed Aug 10 16:50:04 2011 -0400
@@ -920,7 +920,7 @@
view.overview_close.show();
view.overview_viewport.append(tile.canvas);
view.overview_highlight.show().height(tile.canvas.height());
- view.overview_viewport.height(tile.canvas.height() + view.overview_box.height());
+ view.overview_viewport.height(tile.canvas.height() + view.overview_box.outerHeight());
view.resize_window();
// Update view, track states.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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