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annotate rgWebLogo3.xml @ 3:3179d17dc6e5 draft
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 15:53:33 -0400 |
| parents | 76426785ae1c |
| children | dc25a5169a91 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rgweblogo3" name="Sequence Logo" version="0.4"> |
| 2 <description>generator for fasta (eg Clustal alignments)</description> | |
| 3 <requirements> | |
| 1 | 4 <requirement type="package" version="1.7.1">numpy</requirement> |
| 0 | 5 <requirement type="package" version="3.3">weblogo</requirement> |
| 6 <requirement type="package" version="9.10">ghostscript</requirement> | |
| 7 </requirements> | |
| 8 <command interpreter="python"> | |
| 9 rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units" | |
| 10 #if $range.mode == 'part' | |
| 11 -l "$range.seqstart" -u "$range.seqend" | |
| 12 #end if | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <page> | |
| 16 <param format="fasta" name="input" type="data" label="Fasta File" /> | |
|
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3179d17dc6e5
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
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changeset
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17 <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" /> |
| 0 | 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> | |
|
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76426785ae1c
planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
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changeset
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24 <option value="logodata">Text (shows the detailed calculations for each position - no image)</option> |
| 0 | 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 | |
| 46 | |
| 47 <conditional name="range"> | |
| 48 <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> | |
| 49 <option value="complete" selected="true">complete sequence</option> | |
| 50 <option value="part">Only use a part of the sequence</option> | |
| 51 </param> | |
| 52 <when value="complete"> | |
| 53 </when> | |
| 54 <when value="part"> | |
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3179d17dc6e5
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
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diff
changeset
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55 <param name="seqstart" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" |
| 0 | 56 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> |
| 57 </param> | |
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3179d17dc6e5
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
devteam
parents:
2
diff
changeset
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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" > |
| 0 | 59 </param> |
| 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 </page> | |
| 68 </inputs> | |
| 69 <outputs> | |
| 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" /> | |
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76426785ae1c
planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents:
1
diff
changeset
|
76 <when input="outformat" value="logodata" format="txt" /> |
| 0 | 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 | |
| 104 **Note** | |
| 105 | |
| 106 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history. | |
| 107 | |
| 108 It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed | |
| 109 it in to this tool. | |
| 110 | |
| 111 A typical output looks like this | |
| 112 | |
| 113 .. image:: ${static_path}/images/rgWebLogo3_test.jpg | |
| 114 | |
| 115 ---- | |
| 116 | |
| 117 **Warning about input Fasta format files** | |
| 118 | |
| 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 | |
| 120 and refuse to call the weblogo3 executable if irregular length sequences are detected. | |
| 121 | |
| 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 | |
| 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 | |
| 124 sequences are the same length! | |
| 125 | |
| 126 ---- | |
| 127 | |
| 128 **Attribution** | |
| 129 | |
| 130 Weblogo attribution and associated documentation are available at Weblogo3_ | |
| 131 | |
| 132 This Galaxy wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts | |
| 133 | |
| 134 .. _Weblogo3: http://weblogo.berkeley.edu/ | |
| 135 | |
| 136 .. _LGPL: http://www.gnu.org/copyleft/lesser.html | |
| 137 | |
| 138 </help> | |
| 139 | |
| 140 </tool> | |
| 141 | |
| 142 |