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rollback. sorry, removed the wrong files

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This commit is contained in:
Jianbin He
2007-06-04 14:18:13 +00:00
parent 251b052221
commit a6d5eaa93f
3 changed files with 163 additions and 0 deletions
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tools/visualization/build_ucsc_custom_track.py
Executable
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#!/usr/bin/env python2.4
"""
Build a UCSC genome browser custom track file
"""
import sys, os
args = sys.argv[1:]
out_fname = args.pop(0)
out = open( out_fname, "w" )
num_tracks = 0
while args:
# Suck in one dataset worth of arguments
in_fname = args.pop(0)
type = args.pop(0)
colspec = args.pop(0)
name = args.pop(0)
description = args.pop(0)
color = args.pop(0).replace( '-', ',' )
visibility = args.pop(0)
# Do the work
if type == "wig":
print >> out, '''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s''' \
% ( name, description, color, visibility )
for line in open( in_fname ):
print >> out, line,
print >> out
elif type == "bed":
print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \
% ( name, description, color, visibility )
for line in open( in_fname ):
print >> out, line,
print >> out
else:
# Assume type is interval (don't pass this script anything else!)
c, s, e, st = map( int, colspec.split( "," ) )
print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \
% ( name, description, color, visibility )
i = 0
for line in open( in_fname ):
if line.startswith( "#" ):
continue
fields = line.split( "\t" )
if st > 0 and st < len( fields ):
print >> out, "%s\t%s\t%s\t%d\t0\t%s" % ( fields[c], fields[s], fields[e], i, fields[st] )
else:
print >> out, "%s\t%s\t%s" % ( fields[c], fields[s], fields[e] )
i += 1
print >> out
num_tracks += 1
out.close()
print "Generated a custom track containing %d subtracks." % num_tracks
tools/visualization/build_ucsc_custom_track.xml
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<tool id="build_ucsc_custom_track_1" name="Build custom track">
<description>for UCSC genome browser</description>
<command interpreter="python2.4">
build_ucsc_custom_track.py
"$out_file1"
#for $t in $tracks
"${t.input.file_name}"
"${t.input.ext}"
#if $t.input.ext == "interval"
${t.input.metadata.chromCol},${t.input.metadata.startCol},${t.input.metadata.endCol},${t.input.metadata.strandCol}
#else
"NA"
#end if
"${t.name}"
"${t.description}"
"${t.color}"
"${t.visibility}"
#end for
</command>
<inputs>
<repeat name="tracks" title="Track">
<param name="input" type="data" format="interval,wig" label="Dataset"/>
<param name="name" type="text" size="15" value="User Track">
<validator type="length" max="15"/>
</param>
<param name="description" type="text" value="User Supplied Track (from Galaxy)">
<validator type="length" max="60"/>
</param>
<param label="Color" name="color" type="select">
<option selected="yes" value="0-0-0">Black</option>
<option value="255-0-0">Red</option>
<option value="0-255-0">Green</option>
<option value="0-0-255">Blue</option>
<option value="255-0-255">Magenta</option>
<option value="0-255-255">Cyan</option>
<option value="255-215-0">Gold</option>
<option value="160-32-240">Purple</option>
<option value="255-140-0">Orange</option>
<option value="255-20-147">Pink</option>
<option value="92-51-23">Dark Chocolate</option>
<option value="85-107-47">Olive green</option>
</param>
<param label="Visibility" name="visibility" type="select">
<option selected="yes" value="1">Dense</option>
<option value="2">Full</option>
<option value="3">Pack</option>
<option value="4">Squish</option>
<option value="0">Hide</option>
</param>
</repeat>
</inputs>
<outputs>
<data format="customtrack" name="out_file1" />
</outputs>
<!--
<tests>
<test>
<param name="primary" value="customTrack1.bed" />
<param name="primary_color" value="0-0-0" />
<param name="primary_visib" value="1" />
<param name="primary_name" value="customTrack1.bed" />
<param name="newdata" value="customTrack2.bed" />
<param name="status" value="1" />
<param name="Color" value="255-0-0" />
<param name="Visibility" value="2" />
<param name="other_names" value="customTrack2.bed" />
<output name="out_file1" file="customTrack_output.dat" />
</test>
</tests>
-->
<help>
**Info**
This tool displays the selected datasets with their custom track attributes (if any) in the UCSC genome browser.
This tool allows you to set the **Color** and **Visibility** attributes and you can edit the **Name** attribute of the dataset by clicking on **"edit attributes"** button (pencil icon) next to the dataset name in the history panel.
Please note that the primary dataset in step 1 of the tool sets the database build for the datasets in following steps. For example, if your first dataset belogs to hg18, you will only be able to select hg18 associated datasets on the next step.
</help>
<code file="build_ucsc_custom_track_code.py" />
</tool>
tools/visualization/build_ucsc_custom_track_code.py
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# runs after the job (and after the default post-filter)
from sets import Set as set
def validate_input( trans, error_map, param_values, page_param_map ):
dbkeys = set()
tracks = param_values['tracks']
for track in tracks:
if track['input'] is not None:
dbkeys.add( track['input'].dbkey )
if len( dbkeys ) > 1:
# FIXME: Should be able to assume error map structure is created
if 'tracks' not in error_map:
error_map['tracks'] = [ dict() for t in tracks ]
for i in range( len( tracks ) ):
error_map['tracks'][i]['input'] = \
"All datasets must belong to same genomic build"