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Update GMAJ to latest version. This now accepts BED as input for annotations.

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TODO: Allow annotations to be specified for all species in the file, not just the
'primary' organism (as specified by the dbkey). Metadata for sequences will need to be
fleshed out more first (i.e. store all species present in the file).
This commit is contained in:
Daniel Blankenberg
2007-07-25 20:39:16 +00:00
parent 88e186e19b
commit a3390c3dc4
4 changed files with 8 additions and 8 deletions
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lib/galaxy/datatypes/images.py
+1 -1
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@@ -18,7 +18,7 @@ class Image( data.Data ):
class Gmaj( data.Data ):
"""Class describing a GMAJ Applet"""
def set_peek( self, dataset ):
dataset.peek = "<p align=\"center\"><applet code=\"edu.psu.bx.gmaj.MajApplet.class\" archive=\"static/gmaj/gmaj.jar\" width=\"200\" height=\"30\" align=\"middle\"> <param name=bundle value=\"display?id="+str(dataset.id)+"&tofile=yes&toext=.zip\"> <param name=buttonlabel value=\"Launch GMAJ\"><param name=nobutton value=\"false\"><param name=urlpause value=\"100\"><param name=debug value=\"false\"><i>Your browser is not responding to the &lt;applet&gt; tag.</i></applet></p>"
dataset.peek = "<p align=\"center\"><applet code=\"edu.psu.bx.gmaj.MajApplet.class\" archive=\"/static/gmaj/gmaj.jar\" width=\"200\" height=\"30\" align=\"middle\"> <param name=bundle value=\"display?id="+str(dataset.id)+"&tofile=yes&toext=.zip\"> <param name=buttonlabel value=\"Launch GMAJ\"><param name=nobutton value=\"false\"><param name=urlpause value=\"100\"><param name=debug value=\"false\"><i>Your browser is not responding to the &lt;applet&gt; tag.</i></applet></p>"
dataset.blurb = 'GMAJ Multiple Alignment Viewer'
def display_peek(self, dataset):
static/gmaj/gmaj.jar
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tools/visualization/GMAJ.py
+1 -1
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@@ -43,7 +43,7 @@ out_file = zipfile.ZipFile(out_file, "w") #, ZIP_DEFLATED)
#determine organisms located in maf file.
species = get_species_names( maf_file )
GMAJ_str = "#:gmaj\n\ntitle = \"GMAJ through Galaxy\"\nalignfile = input.maf\n"
GMAJ_str = "#:gmaj\n\ntitle = \"GMAJ through Galaxy\"\nalignfile = input.maf\nnowarn = bed_blocks bed_thick bed_name repeat_type_missing bed_name_prefix\ntabext = .%s\n" % (dbkey)
if dbkey in species and len(species[dbkey])>0:
GMAJ_str = GMAJ_str + "refseq = "+dbkey+"."+species[dbkey][0]+"\n"
else:
tools/visualization/GMAJ.xml
+6 -6
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@@ -3,17 +3,17 @@
<command interpreter="python2.4">GMAJ.py $out_file1 $maf_input $dbkey $exons_file $highlights_file $underlays_file $repeats_file $links_file</command>
<inputs>
<param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/>
<param name="exons_file" type="data" format="txt" label="Exons File" optional="True"/>
<param name="highlights_file" type="data" format="txt" label="Highlights File" optional="True"/>
<param name="underlays_file" type="data" format="txt" label="Underlays File" optional="True"/>
<param name="repeats_file" type="data" format="txt" label="Repeats File" optional="True"/>
<param name="links_file" type="data" format="txt" label="Links File" optional="True"/>
<param name="exons_file" type="data" format="bed" label="Exons File" optional="True"/>
<param name="highlights_file" type="data" format="bed" label="Highlights File" optional="True"/>
<param name="underlays_file" type="data" format="bed" label="Underlays File" optional="True"/>
<param name="repeats_file" type="data" format="bed" label="Repeats File" optional="True"/>
<param name="links_file" type="data" format="bed" label="Links File" optional="True"/>
</inputs>
<outputs>
<data name="out_file1" format="gmaj.zip"/>
</outputs>
<help>
You can use this tool to view a set of MAF alignments. You may also include optional additional information about the primary organism, please see the documentation for proper file formats.
You can use this tool to view a set of MAF alignments. You may also include optional additional information about the primary organism in the BED format.
For detailed information on GMAJ, click here_.