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comparison rgWebLogo3.xml @ 1:d16cc2d33359 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:35:51 -0400
parents f64b81fda062
children 13045f6015cb
comparison
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0:f64b81fda062 1:d16cc2d33359
1 <tool id="rgweblogo3" name="Sequence Logo" version="0.4"> 1 <tool id="rgweblogo3" name="Sequence Logo" version="0.4">
2 <description>generator for fasta (eg Clustal alignments)</description> 2 <description>generator for fasta (eg Clustal alignments)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement>
4 <requirement type="package" version="3.3">weblogo</requirement> 5 <requirement type="package" version="3.3">weblogo</requirement>
5 <requirement type="package" version="9.10">ghostscript</requirement> 6 <requirement type="package" version="9.10">ghostscript</requirement>
6 </requirements> 7 </requirements>
7 <command interpreter="python"> 8 <command interpreter="python">
8 rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units" 9 rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"
11 #end if 12 #end if
12 </command> 13 </command>
13 <inputs> 14 <inputs>
14 <page> 15 <page>
15 <param format="fasta" name="input" type="data" label="Fasta File" /> 16 <param format="fasta" name="input" type="data" label="Fasta File" />
16 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" /> 17 <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" />
17 <param name="outformat" type="select" label="Output format for image (or text report)" > 18 <param name="outformat" type="select" label="Output format for image (or text report)" >
18 <option value="png" selected="True">PNG screen quality</option> 19 <option value="png" selected="True">PNG screen quality</option>
19 <option value="png_print">High quality printable PNG</option> 20 <option value="png_print">High quality printable PNG</option>
20 <option value="pdf">PDF</option> 21 <option value="pdf">PDF</option>
21 <option value="jpeg">JPG</option> 22 <option value="jpeg">JPG</option>
22 <option value="eps">EPS</option> 23 <option value="eps">EPS</option>
23 <option value="txt">Text (shows the detailed calculations for each position - no image)</option> 24 <option value="logodata">Text (shows the detailed calculations for each position - no image)</option>
24 </param> 25 </param>
25 <param name="units" type="select" label="Display Units" 26 <param name="units" type="select" label="Display Units"
26 help="What the height of each logo element depicts - eg bits of entropy (default)"> 27 help="What the height of each logo element depicts - eg bits of entropy (default)">
27 <option value="bits" selected="True">Entropy (bits)</option> 28 <option value="bits" selected="True">Entropy (bits)</option>
28 <option value="probability">Probability</option> 29 <option value="probability">Probability</option>
49 <option value="part">Only use a part of the sequence</option> 50 <option value="part">Only use a part of the sequence</option>
50 </param> 51 </param>
51 <when value="complete"> 52 <when value="complete">
52 </when> 53 </when>
53 <when value="part"> 54 <when value="part">
54 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 55 <param name="seqstart" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!"
55 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> 56 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
56 </param> 57 </param>
57 <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" > 58 <param name="seqend" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
58 </param> 59 </param>
59 </when> 60 </when>
60 </conditional> 61 </conditional>
61 <param name="size" type="select" label="Output weblogo size" > 62 <param name="size" type="select" label="Output weblogo size" >
62 <option value="large" selected="True">Large</option> 63 <option value="large" selected="True">Large</option>
70 <change_format> 71 <change_format>
71 <when input="outformat" value="png_print" format="png" /> 72 <when input="outformat" value="png_print" format="png" />
72 <when input="outformat" value="png" format="png" /> 73 <when input="outformat" value="png" format="png" />
73 <when input="outformat" value="jpeg" format="jpg" /> 74 <when input="outformat" value="jpeg" format="jpg" />
74 <when input="outformat" value="eps" format="eps" /> 75 <when input="outformat" value="eps" format="eps" />
75 <when input="outformat" value="txt" format="txt" /> 76 <when input="outformat" value="logodata" format="txt" />
76 </change_format> 77 </change_format>
77 </data> 78 </data>
78 </outputs> 79 </outputs>
79 <tests> 80 <tests>
80 <test> 81 <test>