/tools/rgenetics/rgWebLogo3.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 138 lines · 117 code · 21 blank · 0 comment · 0 complexity · 8a993c202a96571d781ff35b934e02e5 MD5 · raw file
- <tool id="rgweblogo3" name="Sequence Logo" version="0.4">
- <requirements><requirement type="package">weblogo</requirement></requirements>
- <description>generator for fasta (eg Clustal alignments)</description>
- <command interpreter="python">
- rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"
- #if $range.mode == 'part'
- -l "$range.seqstart" -u "$range.seqend"
- #end if
- </command>
- <inputs>
- <page>
- <param format="fasta" name="input" type="data" label="Fasta File" />
- <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" />
- <param name="outformat" type="select" label="Output format for image (or text report)" >
- <option value="png" selected="True">PNG screen quality</option>
- <option value="png_print">High quality printable PNG</option>
- <option value="pdf">PDF</option>
- <option value="jpeg">JPG</option>
- <option value="eps">EPS</option>
- <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
- </param>
- <param name="units" type="select" label="Display Units"
- help="What the height of each logo element depicts - eg bits of entropy (default)">
- <option value="bits" selected="True">Entropy (bits)</option>
- <option value="probability">Probability</option>
- <option value="nats">Nats</option>
- <option value="kT">kT</option>
- <option value="kJ/mol">kJ/mol</option>
- <option value="kcal/mol">kcal/mol</option>
- </param>
- <param name="colours" type="select" label="Colour scheme for output Sequence Logo"
- help="Note that some of these only make sense for protein sequences!">
- <option value="auto" selected="True">Default automatic colour selection</option>
- <option value="base pairing">Base pairing</option>
- <option value="charge">Charge colours</option>
- <option value="chemistry">Chemistry colours</option>
- <option value="classic">Classical colours</option>
- <option value="hydrophobicity">Hydrophobicity</option>
- <option value="monochrome">monochrome</option>
- </param>
-
- <conditional name="range">
- <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
- <option value="complete" selected="true">complete sequence</option>
- <option value="part">Only use a part of the sequence</option>
- </param>
- <when value="complete">
- </when>
- <when value="part">
- <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!"
- label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
- </param>
- <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" >
- </param>
- </when>
- </conditional>
- <param name="size" type="select" label="Output weblogo size" >
- <option value="large" selected="True">Large</option>
- <option value="medium">Medium</option>
- <option value="small">Small</option>
- </param>
- </page>
- </inputs>
- <outputs>
- <data format="pdf" name="output" label="${logoname}_output.${outformat}">
- <change_format>
- <when input="outformat" value="png_print" format="png" />
- <when input="outformat" value="png" format="png" />
- <when input="outformat" value="jpeg" format="jpg" />
- <when input="outformat" value="eps" format="eps" />
- <when input="outformat" value="txt" format="txt" />
- </change_format>
- </data>
- </outputs>
- <tests>
- <test>
- <param name="input" value="rgClustal_testout.fasta" />
- <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
- <param name = "outformat" value="jpeg" />
- <param name = "mode" value="complete" />
- <param name = "size" value="medium" />
- <param name = "colours" value="auto" />
- <param name = "units" value="bits" />
- <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" />
- </test>
- <test>
- <param name="input" value="rgClustal_testout.fasta" />
- <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
- <param name = "outformat" value="png" />
- <param name = "mode" value="complete" />
- <param name = "size" value="medium" />
- <param name = "colours" value="auto" />
- <param name = "units" value="probability" />
- <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" />
- </test>
- </tests>
- <help>
- **Note**
- This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
- It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
- it in to this tool.
- A typical output looks like this
- .. image:: ${static_path}/images/rgWebLogo3_test.jpg
- ----
- **Warning about input Fasta format files**
- 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
- and refuse to call the weblogo3 executable if irregular length sequences are detected.
- 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
- 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
- sequences are the same length!
- ----
- **Attribution**
- Weblogo attribution and associated documentation are available at Weblogo3_
- 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
- .. _Weblogo3: http://weblogo.berkeley.edu/
- .. _LGPL: http://www.gnu.org/copyleft/lesser.html
- </help>
- </tool>