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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 commit d0f167e74e705788adcd9c846db011aee490074b
author iuc
date Fri, 17 Nov 2017 09:38:19 -0500
parents d16cc2d33359
children
comparison
equal deleted inserted replaced
2:ced02f5334a0 3:13045f6015cb
1 <tool id="rgweblogo3" name="Sequence Logo" version="0.4"> 1 <tool id="rgweblogo3" name="Sequence Logo" version="3.5.0">
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="3.5.0">weblogo</requirement>
5 <requirement type="package" version="3.3">weblogo</requirement> 5 </requirements>
6 <requirement type="package" version="9.10">ghostscript</requirement> 6 <command><![CDATA[
7 </requirements> 7 python '$__tool_directory__/rgWebLogo3.py'
8 <command interpreter="python"> 8 -F $outformat
9 rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units" 9 -s $size
10 #if $range.mode == 'part' 10 -i '$input'
11 -l "$range.seqstart" -u "$range.seqend" 11 -o '$output'
12 #end if 12 -t '$logoname'
13 </command> 13 -c '$colours'
14 <inputs> 14 -U '$units'
15 <page>
16 <param format="fasta" name="input" type="data" label="Fasta File" />
17 <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" />
18 <param name="outformat" type="select" label="Output format for image (or text report)" >
19 <option value="png" selected="True">PNG screen quality</option>
20 <option value="png_print">High quality printable PNG</option>
21 <option value="pdf">PDF</option>
22 <option value="jpeg">JPG</option>
23 <option value="eps">EPS</option>
24 <option value="logodata">Text (shows the detailed calculations for each position - no image)</option>
25 </param>
26 <param name="units" type="select" label="Display Units"
27 help="What the height of each logo element depicts - eg bits of entropy (default)">
28 <option value="bits" selected="True">Entropy (bits)</option>
29 <option value="probability">Probability</option>
30 <option value="nats">Nats</option>
31 <option value="kT">kT</option>
32 <option value="kJ/mol">kJ/mol</option>
33 <option value="kcal/mol">kcal/mol</option>
34 </param>
35 <param name="colours" type="select" label="Colour scheme for output Sequence Logo"
36 help="Note that some of these only make sense for protein sequences!">
37 <option value="auto" selected="True">Default automatic colour selection</option>
38 <option value="base pairing">Base pairing</option>
39 <option value="charge">Charge colours</option>
40 <option value="chemistry">Chemistry colours</option>
41 <option value="classic">Classical colours</option>
42 <option value="hydrophobicity">Hydrophobicity</option>
43 <option value="monochrome">monochrome</option>
44 </param>
45 15
46 16 #if $range.mode == 'part'
47 <conditional name="range"> 17 -l '$range.seqstart' -u '$range.seqend'
48 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> 18 #end if
49 <option value="complete" selected="true">complete sequence</option> 19 ]]></command>
50 <option value="part">Only use a part of the sequence</option> 20 <inputs>
21 <param format="fasta" name="input" type="data" label="Fasta File" />
22 <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" />
23 <param name="outformat" type="select" label="Output format for image (or text report)" >
24 <option value="png" selected="True">PNG screen quality</option>
25 <option value="png_print">High quality printable PNG</option>
26 <option value="pdf">PDF</option>
27 <option value="jpeg">JPG</option>
28 <option value="eps">EPS</option>
29 <option value="logodata">Text (shows the detailed calculations for each position - no image)</option>
51 </param> 30 </param>
52 <when value="complete"> 31 <param name="units" type="select" label="Display Units" help="What the height of each logo element depicts - eg bits of entropy (default)">
53 </when> 32 <option value="bits" selected="True">Entropy (bits)</option>
54 <when value="part"> 33 <option value="probability">Probability</option>
55 <param name="seqstart" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 34 <option value="nats">Nats</option>
56 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> 35 <option value="kT">kT</option>
57 </param> 36 <option value="kJ/mol">kJ/mol</option>
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" > 37 <option value="kcal/mol">kcal/mol</option>
59 </param> 38 </param>
60 </when> 39 <param name="colours" type="select" label="Colour scheme for output Sequence Logo"
61 </conditional> 40 help="Note that some of these only make sense for protein sequences!">
62 <param name="size" type="select" label="Output weblogo size" > 41 <option value="auto" selected="True">Default automatic colour selection</option>
63 <option value="large" selected="True">Large</option> 42 <option value="base pairing">Base pairing</option>
64 <option value="medium">Medium</option> 43 <option value="charge">Charge colours</option>
65 <option value="small">Small</option> 44 <option value="chemistry">Chemistry colours</option>
66 </param> 45 <option value="classic">Classical colours</option>
67 </page> 46 <option value="hydrophobicity">Hydrophobicity</option>
68 </inputs> 47 <option value="monochrome">monochrome</option>
69 <outputs> 48 </param>
70 <data format="pdf" name="output" label="${logoname}_output.${outformat}">
71 <change_format>
72 <when input="outformat" value="png_print" format="png" />
73 <when input="outformat" value="png" format="png" />
74 <when input="outformat" value="jpeg" format="jpg" />
75 <when input="outformat" value="eps" format="eps" />
76 <when input="outformat" value="logodata" format="txt" />
77 </change_format>
78 </data>
79 </outputs>
80 <tests>
81 <test>
82 <param name="input" value="rgClustal_testout.fasta" />
83 <param name="logoname" value="Galaxy/Rgenetics weblogo" />
84 <param name="outformat" value="jpeg" />
85 <param name="mode" value="complete" />
86 <param name="size" value="medium" />
87 <param name="colours" value="auto" />
88 <param name="units" value="bits" />
89 <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" />
90 </test>
91 <test>
92 <param name="input" value="rgClustal_testout.fasta" />
93 <param name="logoname" value="Galaxy/Rgenetics weblogo" />
94 <param name="outformat" value="png" />
95 <param name="mode" value="complete" />
96 <param name="size" value="medium" />
97 <param name="colours" value="auto" />
98 <param name="units" value="probability" />
99 <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" />
100 </test>
101 </tests>
102 <help>
103 49
50 <conditional name="range">
51 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
52 <option value="complete" selected="true">complete sequence</option>
53 <option value="part">Only use a part of the sequence</option>
54 </param>
55 <when value="complete" />
56 <when value="part">
57 <param name="seqstart" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!"
58 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo" />
59 <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" />
60 </when>
61 </conditional>
62 <param name="size" type="select" label="Output weblogo size" >
63 <option value="large" selected="True">Large</option>
64 <option value="medium">Medium</option>
65 <option value="small">Small</option>
66 </param>
67 </inputs>
68 <outputs>
69 <data format="pdf" name="output" label="${logoname}_output.${outformat}">
70 <change_format>
71 <when input="outformat" value="png_print" format="png" />
72 <when input="outformat" value="png" format="png" />
73 <when input="outformat" value="jpeg" format="jpg" />
74 <when input="outformat" value="eps" format="eps" />
75 <when input="outformat" value="logodata" format="txt" />
76 </change_format>
77 </data>
78 </outputs>
79 <tests>
80 <test>
81 <param name="input" value="rgClustal_testout.fasta" />
82 <param name="logoname" value="Galaxy/Rgenetics weblogo" />
83 <param name="outformat" value="jpeg" />
84 <param name="mode" value="complete" />
85 <param name="size" value="medium" />
86 <param name="colours" value="auto" />
87 <param name="units" value="bits" />
88 <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" />
89 </test>
90 <test>
91 <param name="input" value="rgClustal_testout.fasta" />
92 <param name="logoname" value="Galaxy/Rgenetics weblogo" />
93 <param name="outformat" value="png" />
94 <param name="mode" value="complete" />
95 <param name="size" value="medium" />
96 <param name="colours" value="auto" />
97 <param name="units" value="probability" />
98 <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" />
99 </test>
100 </tests>
101 <help><![CDATA[
104 **Note** 102 **Note**
105 103
106 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history. 104 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
107 105
108 It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed 106 It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
117 **Warning about input Fasta format files** 115 **Warning about input Fasta format files**
118 116
119 The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning 117 The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning
120 and refuse to call the weblogo3 executable if irregular length sequences are detected. 118 and refuse to call the weblogo3 executable if irregular length sequences are detected.
121 119
122 Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file 120 Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file
123 a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta 121 a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta
124 sequences are the same length! 122 sequences are the same length!
125 123
126 ---- 124 ----
127 125
128 **Attribution** 126 **Attribution**
133 131
134 .. _Weblogo3: http://weblogo.berkeley.edu/ 132 .. _Weblogo3: http://weblogo.berkeley.edu/
135 133
136 .. _LGPL: http://www.gnu.org/copyleft/lesser.html 134 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
137 135
138 </help> 136 ]]></help>
139 137 <citations>
138 <citation type="doi">10.1101/gr.849004</citation>
139 </citations>
140 </tool> 140 </tool>
141
142