Mercurial > repos > iuc > progressivemauve

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
author iuc
date Wed, 17 Aug 2016 14:46:55 -0400
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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1 <?xml version="1.0"?>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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2 <tool id="xmfa2gff3" name="Convert XMFA to gapped GFF3" version="@WRAPPER_VERSION@.0">
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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3 <description></description>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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4 <macros>
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5 <import>macros.xml</import>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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6 </macros>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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7 <expand macro="requirements"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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8 <expand macro="stdio"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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9 <version_command>python xmfa2gff3.py --version</version_command>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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10 <command interpreter="python"><![CDATA[
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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11 xmfa2gff3.py
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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12 $xmfa
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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13 --window_size $window_size
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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14 --relative_to $relative_to
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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15 --sequences
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16 #for file in $sequences:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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17 "${file}"
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18 #end for
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19 > $output
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20
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21 ]]></command>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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22 <inputs>
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23 <param type="data" format="xmfa" name="xmfa"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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24 label="XMFA MSA" />
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25
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26 <param type="data" format="fasta" name="sequences" multiple="True"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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27 label="Select sequences used in progressiveMauve alignment"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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28 help="Should be provided in the same order as in original progressiveMauve run"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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29
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30 <param type="integer" label="Window Size" value="100" name="window_size"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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31 help="maximum length of a match_part feature. Lower number = larger GFF output" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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32
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33 <param type="integer" label="Generate relative to Nth sequence in XMFA file" value="1" name="relative_to"
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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34 help="progressiveMauve (un)helpfully strips original sequence IDs and replaces with integer numbers. This option lets you generate the alignment relative to e.g. the second genome if you wished to display against that base sequence" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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35 </inputs>
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36 <outputs>
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37 <data format="gff3" name="output">
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38 </data>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="xmfa" value="1.xmfa"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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43 <param name="sequences" value="karma.fa,phagey.fa" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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44 <param name="window_size" value="10" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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45 <param name="relative_to" value="1" />
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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46 <output name="output" file="1.gff3"/>
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 What it does
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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51 ============
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52
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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53 XMFA Alignments are great, but now you need a way to visualize this data!
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54
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55 This tool provides a conversion step to GFF3 formatted output consiting of
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56 ``match``es and ``match_part``s with scores indicating percent identity over
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57 that chunk of sequence.
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58
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59 A rendering of the output GFF3 file in JBrowse is shown below:
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60
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61 .. image:: $PATH_TO_IMAGES/xmfa2gff3.png
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62
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63 ]]></help>
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64 <citations>
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65 </citations>
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66 </tool>