1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/429c1054c13e/
changeset: 429c1054c13e
user: jgoecks
date: 2012-08-23 21:58:11
summary: Require pileup format as input to pileup parser tool.
affected #: 1 file
diff -r 3bd47802bff7946958b0a616e3d42aef50c63277 -r 429c1054c13e9c2206ccd4bc3dfd1ca1fa75973c tools/samtools/pileup_parser.xml
--- a/tools/samtools/pileup_parser.xml
+++ b/tools/samtools/pileup_parser.xml
@@ -7,7 +7,7 @@
#end if#
</command><inputs>
- <param name="input" type="data" format="tabular" label="Select dataset"/>
+ <param name="input" type="data" format="pileup" label="Select dataset"/><conditional name="pileup_type"><param name="type_select" type="select" label="which contains" help="See "Types of pileup datasets" below for examples"><option value="six" selected="true">Pileup with six columns (simple)</option>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/3bd47802bff7/
changeset: 3bd47802bff7
user: jgoecks
date: 2012-08-23 19:56:34
summary: Trackster: for feature tracks, only draw name if available.
affected #: 1 file
diff -r c06d0ea23c902e13a5d38ed56ab8cad53130fea5 -r 3bd47802bff7946958b0a616e3d42aef50c63277 static/scripts/viz/trackster.js
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -5690,7 +5690,7 @@
ctx.globalAlpha = 1;
// Draw label for Pack mode.
- if (mode === "Pack" && feature_start > tile_low) {
+ if (feature_name && mode === "Pack" && feature_start > tile_low) {
ctx.fillStyle = label_color;
// FIXME: assumption here that the entire view starts at 0
if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/146d0f4c29de/
changeset: 146d0f4c29de
user: jgoecks
date: 2012-08-23 15:04:08
summary: Fix for handling missing quality values in VCF data provider + some whitespace. Thanks to Jim Johnson for fix.
affected #: 1 file
diff -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 -r 146d0f4c29decefb441a7133b4aa16442afdacb1 lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -625,7 +625,8 @@
end = start + len( new_seq )
# Pack line.
- payload = [ hash( line ),
+ payload = [
+ hash( line ),
start,
end,
# ID:
@@ -634,7 +635,8 @@
# TODO? VCF does not have strand, so default to positive.
"+",
new_seq,
- float( feature[5] ) ]
+ None if feature[5] == '.' else float( feature[5] )
+ ]
rval.append(payload)
return { 'data': rval, 'message': message }
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/dd8a939cf0a2/
changeset: dd8a939cf0a2
user: jgoecks
date: 2012-08-23 04:54:54
summary: Update datatypes conf sample to include bedgraph to bigwig converter.
affected #: 1 file
diff -r f0e26a4f7dd91d9a632913ae450e285e37a9a302 -r dd8a939cf0a26ea9e3cb969297bbfe7d749e88f7 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -23,7 +23,9 @@
<display file="genetrack.xml" /><display file="igb/bed.xml" /></datatype>
- <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" />
+ <datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true">
+ <converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/>
+ </datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"><converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/695159af542b/
changeset: 695159af542b
user: dannon
date: 2012-08-22 22:12:59
summary: Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.
affected #: 36 files
Diff too large to display.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/bf6517b2b336/
changeset: bf6517b2b336
user: richard_burhans
date: 2012-08-22 21:31:23
summary: name change: _BX main_ browser -> _BX_ table browser
affected #: 1 file
diff -r 863e1150c85b7383a1b136c9b3c9376da81bc16b -r bf6517b2b336113964fe90ef74b6db333ee97f63 tools/data_source/bx_browser.xml
--- a/tools/data_source/bx_browser.xml
+++ b/tools/data_source/bx_browser.xml
@@ -4,8 +4,8 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
-<tool name="BX main" id="bx_browser" tool_type="data_source">
- <description>browser</description>
+<tool name="BX" id="bx_browser" tool_type="data_source">
+ <description>table browser</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command><inputs action="http://main.genome-browser.bx.psu.edu/cgi-bin/hgTables" check_values="false" method="get"><display>go to BX Browser $GALAXY_URL</display>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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