Mercurial > repos > fubar > weblogo3
annotate rgweblogo/rgWebLogo3.xml @ 14:a75696764683 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 25 Sep 2013 23:31:04 -0400 |
| parents | aac389ef2849 |
| children |
| rev | line source |
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| 3 | 1 <tool id="rgweblogo3" name="Sequence Logo" version="0.5"> |
| 2 <stdio> | |
| 8 | 3 <regex match=".*" source="both" level="warning" description="chatter from weblogo:"/> |
| 3 | 4 </stdio> |
| 5 <requirements> | |
| 6 <requirement type="package" version="3.3">package_weblogo</requirement> | |
| 6 | 7 <requirement type="package" version="1.7.1">numpy</requirement> |
| 5 | 8 <requirement type="package" version="9.07">ghostscript</requirement> |
| 3 | 9 </requirements> |
| 10 <description>Generator from fasta</description> | |
| 11 <command interpreter="python"> | |
| 12 rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units" | |
| 13 #if $range.mode == 'part' | |
| 14 -l "$range.seqstart" -u "$range.seqend" | |
| 15 #end if | |
| 16 </command> | |
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17 <inputs> |
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18 <page> |
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19 <param format="fasta" name="input" type="data" label="Fasta File" /> |
| 3 | 20 <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" /> |
| 21 <param name="outformat" type="select" label="Output format for image (or text report)" > | |
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22 <option value="png" selected="True">PNG screen quality</option> |
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23 <option value="png_print">High quality printable PNG</option> |
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24 <option value="pdf">PDF</option> |
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25 <option value="jpeg">JPG</option> |
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26 <option value="eps">EPS</option> |
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27 <option value="txt">Text (shows the detailed calculations for each position - no image)</option> |
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28 </param> |
| 3 | 29 <param name="units" type="select" label="Display Units" |
| 30 help="What the height of each logo element depicts - eg bits of entropy (default)"> | |
| 31 <option value="bits" selected="True">Entropy (bits)</option> | |
| 32 <option value="probability">Probability</option> | |
| 33 <option value="nats">Nats</option> | |
| 34 <option value="kT">kT</option> | |
| 35 <option value="kJ/mol">kJ/mol</option> | |
| 36 <option value="kcal/mol">kcal/mol</option> | |
| 37 </param> | |
| 38 <param name="colours" type="select" label="Colour scheme for output Sequence Logo" | |
| 39 help="Note that some of these only make sense for protein sequences!"> | |
| 40 <option value="auto" selected="True">Default automatic colour selection</option> | |
| 41 <option value="base pairing">Base pairing</option> | |
| 42 <option value="charge">Charge colours</option> | |
| 43 <option value="chemistry">Chemistry colours</option> | |
| 44 <option value="classic">Classical colours</option> | |
| 45 <option value="hydrophobicity">Hydrophobicity</option> | |
| 46 <option value="monochrome">monochrome</option> | |
| 47 </param> | |
| 48 | |
| 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> | |
| 57 <when value="part"> | |
| 58 <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" | |
| 59 label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> | |
| 60 </param> | |
| 61 <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" > | |
| 62 </param> | |
| 63 </when> | |
| 64 </conditional> | |
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65 <param name="size" type="select" label="Output weblogo size" > |
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66 <option value="large" selected="True">Large</option> |
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67 <option value="medium">Medium</option> |
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68 <option value="small">Small</option> |
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69 </param> |
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70 </page> |
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71 </inputs> |
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72 <outputs> |
| 3 | 73 <data format="pdf" name="output" label="${logoname}.${outformat}"> |
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74 <change_format> |
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75 <when input="outformat" value="png_print" format="png" /> |
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76 <when input="outformat" value="png" format="png" /> |
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77 <when input="outformat" value="jpeg" format="jpg" /> |
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78 <when input="outformat" value="eps" format="eps" /> |
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79 <when input="outformat" value="txt" format="txt" /> |
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80 </change_format> |
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81 </data> |
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82 </outputs> |
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83 <tests> |
| 3 | 84 <test> |
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85 <param name="input" value="rgClustal_testout.fasta" /> |
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86 <param name = "logoname" value="Galaxy/Rgenetics weblogo" /> |
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87 <param name = "outformat" value="jpeg" /> |
| 3 | 88 <param name = "mode" value="complete" /> |
| 89 <param name = "size" value="medium" /> | |
| 90 <param name = "colours" value="auto" /> | |
| 91 <param name = "units" value="bits" /> | |
| 92 <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" /> | |
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93 </test> |
| 3 | 94 <test> |
| 95 <param name="input" value="rgClustal_testout.fasta" /> | |
| 96 <param name = "logoname" value="Galaxy/Rgenetics weblogo" /> | |
| 97 <param name = "outformat" value="png" /> | |
| 98 <param name = "mode" value="complete" /> | |
| 99 <param name = "size" value="medium" /> | |
| 100 <param name = "colours" value="auto" /> | |
| 101 <param name = "units" value="probability" /> | |
| 102 <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" /> | |
| 103 </test> | |
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104 </tests> |
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105 <help> |
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106 |
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107 **Note** |
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108 |
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109 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history. |
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110 |
| 3 | 111 It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed |
| 112 it in to this tool. | |
| 113 | |
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114 A typical output looks like this |
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115 |
| 14 | 116 .. image:: $PATH_TO_IMAGES/rgWebLogo3_test.jpg |
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117 |
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118 ---- |
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119 |
| 3 | 120 **Warning about input Fasta format files** |
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121 |
| 3 | 122 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 |
| 123 and refuse to call the weblogo3 executable if irregular length sequences are detected. | |
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124 |
| 3 | 125 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 |
| 126 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 | |
| 127 sequences are exactly the same length! | |
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128 |
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129 |
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130 **Attribution** |
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131 |
| 3 | 132 Weblogo attribution and associated documentation are available at Weblogo3_ |
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133 |
| 3 | 134 This Galaxy wrapper calls their software so depends on it and their license for your legal comfort. |
| 135 The wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts | |
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136 |
| 3 | 137 .. _Weblogo3: http://weblogo.threeplusone.com/manual.html |
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138 |
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139 .. _LGPL: http://www.gnu.org/copyleft/lesser.html |
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140 |
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141 </help> |
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142 |
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143 </tool> |
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144 |
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145 |