Mercurial > repos > nick > dna_visualizer
annotate literal.xml @ 9:abed07ebeac7
visualize.xml: Text tweak
author | Nick Stoler <nstoler@psu.edu> |
---|---|
date | Sun, 02 Mar 2014 23:55:25 -0500 |
parents | 2d99feb4a8e3 |
children | 54223991334b |
rev | line source |
---|---|
0 | 1 <tool id="visualdna" name="DNA visualizer" version="0.1"> |
2 <description>Visualize DNA with colored pixels.</description> | |
4
16772d7246e0
literal.xml: need to clobber output file
Nick Stoler <nstoler@psu.edu>
parents:
3
diff
changeset
|
3 <command interpreter="python">literal.py $input -o $output -c -s ${width}x${height} |
1
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
4 #if $colors.custom: |
5
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
5 -b $colors.background -G $colors.G -C $colors.C -A $colors.A -T $colors.T |
1
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
6 #end if |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
7 </command> |
0 | 8 <inputs> |
2
1695b2153760
literal.xml: fix size param bug, allow text input
Nick Stoler <nstoler@psu.edu>
parents:
1
diff
changeset
|
9 <param name="input" type="data" format="fasta,text" label="Input sequence" /> |
5
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
10 <param name="width" type="integer" value="512" min="0" max="16384" label="Output image width" help="in pixels (max 16384)" /> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
11 <param name="height" type="integer" value="512" min="0" max="16384" label="Output image height" help="in pixels (max 16384)" /> |
1
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
12 <conditional name="colors"> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
13 <param name="custom" type="select" label="Base colors"> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
14 <option value="" selected="True">Use default colors</option> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
15 <option value="true">Use custom colors</option> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
16 </param> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
17 <when value=""> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
18 <!-- do nothing --> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
19 </when> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
20 <when value="true"> |
5
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
21 <!-- 'G':'255,255,255', 'C':'0,0,255', 'A':'0,255,0', 'T':'255,0,0' --> |
6
0c552e103c93
literal.xml: Small UI, documentation changes
Nick Stoler <nstoler@psu.edu>
parents:
5
diff
changeset
|
22 <param name="background" type="text" value="255,255,255" label="Background RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
0c552e103c93
literal.xml: Small UI, documentation changes
Nick Stoler <nstoler@psu.edu>
parents:
5
diff
changeset
|
23 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
0c552e103c93
literal.xml: Small UI, documentation changes
Nick Stoler <nstoler@psu.edu>
parents:
5
diff
changeset
|
24 </param> |
5
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
25 <param name="G" type="text" value="255,255,255" label="G RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
26 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
27 </param> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
28 <param name="C" type="text" value="0,0,255" label="C RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
29 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
30 </param> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
31 <param name="A" type="text" value="0,255,0" label="A RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
32 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
33 </param> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
34 <param name="T" type="text" value="255,0,0" label="T RGB value" help="Three numbers 0 through 255, separated by commas (no spaces)"> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
35 <validator type="regex" message='Color must be in the form of "R,G,B"'>^[0-9]+,[0-9]+,[0-9]+$</validator> |
58160195728e
Change color setting UI, allow background color setting, limit image size.
Nick Stoler <nstoler@psu.edu>
parents:
4
diff
changeset
|
36 </param> |
1
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
37 </when> |
717a4009675c
literal.xml: adding custom color support
Nick Stoler <nstoler@psu.edu>
parents:
0
diff
changeset
|
38 </conditional> |
0 | 39 </inputs> |
40 <outputs> | |
41 <data name="output" format="png"/> | |
42 </outputs> | |
43 | |
44 <help> | |
45 | |
46 .. class:: infomark | |
47 | |
48 **What it does** | |
49 | |
7 | 50 This tool converts DNA sequence into a PNG image by representing each base with one colored pixel. |
0 | 51 |
52 ----- | |
53 | |
54 .. class:: infomark | |
55 | |
56 **Input Format** | |
57 | |
6
0c552e103c93
literal.xml: Small UI, documentation changes
Nick Stoler <nstoler@psu.edu>
parents:
5
diff
changeset
|
58 The input sequence can be in FASTA format or a plain text file containing only the sequence. Any non-ATGC characters (case-insensitive) will be skipped. In a FASTA file with multiple sequences, all sequences will be used. |
0 | 59 |
60 </help> | |
61 | |
62 </tool> |