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comparison fasta_charges.xml @ 1:054f96a0d0fb draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:41:30 +0000
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0:7443c98a4e3c 1:054f96a0d0fb
1 <tool id="edu.tamu.cpt.tools.charges" name="Charges" version="2.0">
2 <description>colour sequences based on rules</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 '$__tool_directory__/fasta_charges.py'
10 '$svg'
11 @SEQUENCE@
12
13 --width '$width'
14
15 #if $scheme.cs == "default":
16 --aa HSQTNCY AVILMPFWG ERDK
17 --fgColor "#000000" "#000000" "#ffffff"
18 --bgColor "#ffffff" "#999999" "#000000"
19 #elif $scheme.cs == "rb":
20 --aa KR ED HSQTNCYAVILMPFWG
21 --fgColor "#ffffff" "#ffffff" "#000000"
22 --bgColor "#00b0f0" "#fc0000" "#ffffff"
23 #elif $scheme.cs == "rbgb":
24 --aa KR ED P C HSQTNYAVILMFWG
25 --fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000"
26 --bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff"
27 #else:
28 --aa
29 #for group in '$scheme.groups':
30 "$group.aminoAcids"
31 #end for
32 --fgColor
33 #for group in '$scheme.groups':
34 "$group.fgColour"
35 #end for
36 --bgColor
37 #for group in '$scheme.groups':
38 "$group.bgColour"
39 #end for
40 #end if
41
42 > $html ]]>
43 </command>
44 <inputs>
45 <expand macro="input/fasta/protein"/>
46 <param label="Output format" name="svg" type="select">
47 <option value="">HTML</option>
48 <option value="--svg">SVG</option>
49 </param>
50 <conditional name="scheme">
51 <param label="Colour scheme" name="cs" type="select">
52 <option value="default">Default hyrophobic/polar/charged</option>
53 <option value="rb">Positives Blue, Negatives Red</option>
54 <option value="rbgb">Positives Blue, Negatives Red, Prolines Green, Cysteines Brown</option>
55 <option value="custom">Custom Colour Scheme</option>
56 </param>
57 <when value="default"/>
58 <when value="rb"/>
59 <when value="custom">
60 <repeat name="groups" title="Colour Group">
61 <param name="aminoAcids" type="text" label="Amino Acids" help="Amino acids to colour a specific colour"/>
62 <param name="fgColour" type="color" label="Foreground Color"/>
63 <param name="bgColour" type="color" label="Background Color"/>
64 </repeat>
65 </when>
66 </conditional>
67 <param label="Plot width" name="width" type="integer" value="120"/>
68 </inputs>
69 <outputs>
70 <data format="html" name="html">
71 <change_format>
72 <when input="svg" value="--svg" format="svg"/>
73 </change_format>
74 </data>
75 </outputs>
76 <tests>
77 <test>
78 <param name="sequences" value="prot.fa"/>
79 <param name="cs" value="default"/>
80 <param name="width" value="120"/>
81 <output name="html" file="charges.html"/>
82 </test>
83 </tests>
84 <help>
85 **What it does**
86
87 Colors fasta (protein) sequences based on rules, and displays outputs as HTML.
88 </help>
89 <expand macro="citations"/>
90 </tool>