annotate SMART/galaxy/getWigProfile.xml @ 25:7809e72960fe

Deleted selected files
author m-zytnicki
date Mon, 29 Apr 2013 03:29:14 -0400
parents 94ab73e8a190
children 0ab839023fe4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
1 <tool id="getWigProfile" name="get WIG profile">
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 <description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
18
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
3 <requirements>
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
4 <requirement type="set_environment">PYTHONPATH</requirement>
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
5 </requirements>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 <command interpreter="python">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 ../Java/Python/getWigProfile.py -i $formatType.inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 #if $formatType.FormatInputFileName == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 -f bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #elif $formatType.FormatInputFileName == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 -f gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 #elif $formatType.FormatInputFileName == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 -f gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 #elif $formatType.FormatInputFileName == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 -f gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 -w $inputWigFile
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 -p $nbPoints
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 -d $distance
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 $strands
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 -o $outputFilePNG
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 #if $optionSMO.SMO == 'Yes':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 -m $optionSMO.smoothen
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 </command>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 <inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 <conditional name="formatType">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 <param name="FormatInputFileName" type="select" label="Input File Format">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 <param name="inputFileName" format="bed" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 <param name="inputFileName" format="gff" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 <param name="nbPoints" type="integer" value="1000" label="number of points on the x-axis"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 <param name="distance" type="integer" value="0" label="distance around genomic coordinates"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 <param name="strands" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 <conditional name="optionSMO">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 <param name="SMO" type="select" label="smoothen the curve">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 <option value="Yes">Yes</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 <option value="No" selected="true">No</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 <when value="Yes">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 <param name="smoothen" type="integer" value="0"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 <when value="No">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 </inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 <outputs>
18
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
70 <data name="outputFilePNG" format="png" label="[get WIG profile] output file"/>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 </outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
73 <help>
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
74 Computes the average distribution of the WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) along the transcripts given in input, and possibly before and after the transcripts.
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
75
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
76 The main inputs of the functions are a file containing a list of transcripts (or any sets of genomic interval) and a directory containing a set of WIG files (one file per chromosome, or one file per chromosome and per strand). The function then computes the WIG profile of each transcript. The user can also define a region around the transcripts that should also be plotted (in this case, the profile will include the WIG values which overlap with the transcript as well as the 5' and 3' regions). Since the transcript do not necessarily have the same sizes, all profiles will be extended or shrinked to fit in a size which is given by the user. If the resulting profile is a bit bumpy, the user can also smoothen the curve by using a linear smoothing function (the size of the smoothing window is given by the user). Finally, the user may want to plot the WIG data for the opposite strand too (if the strand specific WUG data are available).
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
77 </help>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78 </tool>