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comparison fasta_charges.xml @ 3:a39d312f95c7 draft default tip

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planemo upload commit 83c1184008f5967a8265194a4b3496042827cda1
author cpt
date Fri, 20 Sep 2024 05:36:05 +0000
parents defd34aad2dd
children
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2:defd34aad2dd 3:a39d312f95c7
2 <description>colour sequences based on rules</description> 2 <description>colour sequences based on rules</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 5
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"> </expand>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 '$__tool_directory__/fasta_charges.py' 9 python '$__tool_directory__/fasta_charges.py'
10 '$svg' 10 '$svg'
11 @SEQUENCE@ 11 @SEQUENCE@
12 12
13 --width '$width' 13 --width '$width'
14 14
15 #if $scheme.cs == "default": 15 #if $scheme.cs == "default":
16 --aa HSQTNCY AVILMPFWG ERDK 16 --aa HSQTNCY AVILMPFWG ERDK
17 --fgColor "#000000" "#000000" "#ffffff" 17 --fgColor "#000000" "#000000" "#ffffff"
18 --bgColor "#ffffff" "#999999" "#000000" 18 --bgColor "#ffffff" "#999999" "#000000"
19 #elif $scheme.cs == "rb": 19 #elif $scheme.cs == "rb":
20 --aa KR ED HSQTNCYAVILMPFWG 20 --aa KR ED HSQTNCYAVILMPFWG
21 --fgColor "#ffffff" "#ffffff" "#000000" 21 --fgColor "#ffffff" "#ffffff" "#000000"
22 --bgColor "#00b0f0" "#fc0000" "#ffffff" 22 --bgColor "#00b0f0" "#fc0000" "#ffffff"
23 #elif $scheme.cs == "rbgb": 23 #elif $scheme.cs == "rbgb":
24 --aa KR ED P C HSQTNYAVILMFWG 24 --aa KR ED P C HSQTNYAVILMFWG
25 --fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000" 25 --fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000"
26 --bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff" 26 --bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff"
27 #else: 27 #else:
28 --aa 28 --aa
29 #for group in '$scheme.groups': 29 #for group in $scheme.groups:
30 "$group.aminoAcids" 30 "$group.aminoAcids"
31 #end for 31 #end for
32 --fgColor 32 --fgColor
33 #for group in '$scheme.groups': 33 #for group in $scheme.groups:
34 "$group.fgColour" 34 "$group.fgColour"
35 #end for 35 #end for
36 --bgColor 36 --bgColor
37 #for group in '$scheme.groups': 37 #for group in $scheme.groups:
38 "$group.bgColour" 38 "$group.bgColour"
39 #end for 39 #end for
40 #end if 40 #end if
41 41 ]]></command>
42 > $html ]]>
43 </command>
44 <inputs> 42 <inputs>
45 <expand macro="input/fasta/protein"/> 43 <expand macro="input/fasta/protein"></expand>
46 <param label="Output format" name="svg" type="select"> 44 <label for="output-format">Output format</label>
45 <select id="output-format" name="svg">
47 <option value="">HTML</option> 46 <option value="">HTML</option>
48 <option value="--svg">SVG</option> 47 <option value="--svg">SVG</option>
49 </param> 48 </select>
50 <conditional name="scheme"> 49 <conditional name="scheme">
51 <param label="Colour scheme" name="cs" type="select"> 50 <label for="Colour scheme">Colour scheme</label>
51 <select id="Colour scheme" name="cs">
52 <option value="default">Default hyrophobic/polar/charged</option> 52 <option value="default">Default hyrophobic/polar/charged</option>
53 <option value="rb">Positives Blue, Negatives Red</option> 53 <option value="rb">Positives Blue, Negatives Red</option>
54 <option value="rbgb">Positives Blue, Negatives Red, Prolines Green, Cysteines Brown</option> 54 <option value="rbgb">Positives Blue, Negatives Red, Prolines Green, Cysteines Brown</option>
55 <option value="custom">Custom Colour Scheme</option> 55 <option value="custom">Custom Colour Scheme</option>
56 </param> 56 </select>
57 <when value="default"/> 57 <when value="default"></when>
58 <when value="rb"/> 58 <when value="rb"></when>
59 <when value="custom"> 59 <when value="custom">
60 <repeat name="groups" title="Colour Group"> 60 <repeat name="groups" title="Colour Group">
61 <param name="aminoAcids" type="text" label="Amino Acids" help="Amino acids to colour a specific colour"/> 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"/> 62 <param name="fgColour" type="color" label="Foreground Color"/>
63 <param name="bgColour" type="color" label="Background Color"/> 63 <param name="bgColour" type="color" label="Background Color"/>
67 <param label="Plot width" name="width" type="integer" value="120"/> 67 <param label="Plot width" name="width" type="integer" value="120"/>
68 </inputs> 68 </inputs>
69 <outputs> 69 <outputs>
70 <data format="html" name="html"> 70 <data format="html" name="html">
71 <change_format> 71 <change_format>
72 <when input="svg" value="--svg" format="svg"/> 72 <when input="svg" value="--svg" format="svg"></when>
73 </change_format> 73 </change_format>
74 </data> 74 </data>
75 </outputs> 75 </outputs>
76 <tests> 76 <tests>
77 <test> 77 <test>
78 <param name="sequences" value="prot.fa"/> 78 <param name="sequences" value="prot.fa"/>
79 <param name="cs" value="default"/> 79 <param name="cs" value="default"/>
80 <param name="width" value="120"/> 80 <param name="width" value="120"/>
81 <output name="html" file="charges.html"/> 81 <output name="html" file="charges.html"></output>
82 </test> 82 </test>
83 </tests> 83 </tests>
84 <help> 84 <help>
85 **What it does** 85 **What it does**
86 86
87 Colors fasta (protein) sequences based on rules, and displays outputs as HTML. 87 Colors fasta (protein) sequences based on rules, and displays outputs as HTML.
88 </help> 88 </help>
89 <expand macro="citations"/> 89 <expand macro="citations"></expand>
90 </tool> 90 </tool>