annotate SMART/galaxy/plot.xml @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 <tool id="plot" name="Plot">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 <description>Plot some information from a list of transcripts.</description>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 <command interpreter="python">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 ../Java/Python/plot.py -i $formatType.inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 #if $formatType.FormatInputFileName == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 -f gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 #elif $formatType.FormatInputFileName == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 -f gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 #elif $formatType.FormatInputFileName == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 -f gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 -x $xLabel
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 -y $yLabel
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 -X $XVal
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 -Y $YVal
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 #if $optionLog.log == 'Yes' :
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 -l $optionLog.logOnAxisLabel
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 -s $shape
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 -o $outputFile
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 </command>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 <inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 <conditional name="formatType">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 <param name="FormatInputFileName" type="select" label="Input File Format">
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="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 <param name="inputFileName" format="gff" 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="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 <param name="inputFileName" format="gff2" 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="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 <param name="inputFileName" format="gff3" 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 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 <param name="xLabel" type="text" value="value1" label="x label option" help="Choose one of the tags of 9th column in GFF file to be plotted as X-axis. Warning: You can only choose the tag value is digital."/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 <param name="yLabel" type="text" value="value2" label="y label option" help="Choose one of the tags of 9th column in GFF file to be plotted as Y-axis. You can only choose the tag value is digital."/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 <conditional name="optionLog">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 <param name="log" type="select" label="calculate log option" help="use log on x- or y-axis (write 'x', 'y' or 'xy')">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 <option value="Yes">Yes</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 <option value="No" selected="true">No</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 <when value="Yes">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 <param name="logOnAxisLabel" type="text" value="y" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 <when value="No">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 </inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 <outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 <data name="outputFile" format="png" label="[plot] Output file"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 </outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 </tool>