Mercurial > repos > kuyt002 > mummer_toolsuite

annotate MUMmer/nucmer_coords2ACT_galaxy.xml @ 0:61f30d177448 default tip

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initial commit on Mummer toolsuite on toolshed
author eric
date Tue, 31 Mar 2015 14:19:49 +0200
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61f30d177448 initial commit on Mummer toolsuite on toolshed
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1 <tool id="MUMmer2ACT_tool" name="MUMmer2ACT" version="0.1.alx" force_history_refresh="True">
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2 <description>: convert MUMmer comparison (coords) file to ACT (Artemis)</description>
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3 <command interpreter="perl">
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4 nucmer_coords2ACT_galaxy.pl $in_coords $out_act
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5 </command>
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6 <inputs>
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7 <param name="in_coords" type="data" format="tabular" label="MUMmer coords file to use" help="i.e. a nucmer comparison (coords) file" />
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8 </inputs>
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9 <outputs>
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10 <data name="out_act" format="tabular" label="ACT conversion of coords" />
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11 </outputs>
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12 <requirements>
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13 <!-- <requirement type="perl-script">nucmer_coords2ACT_galaxy.pl</requirement> -->
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14 </requirements>
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15 <tests>
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16 <test>
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17 </test>
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18 </tests>
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19 <help>
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20 |
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21 |
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22
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23 **Info**
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24 --------
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25
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26 This tool will convert the MUMmer comparison file (run MUMmer with the coords option) into a "blast crunch" file
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27 that can be read as a comparison file in Artemic Comparison Tool (ACT).
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28
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29 It will output a single tabular crunch file (save as extension .tab on windows systems).
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30
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31 **Reference/questions/remarks**
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32
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33 - *Conversion perl script and wrapper:* Alex Bossers, CVI of Wageningen UR, The Netherlands.
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36
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37 </help>
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38 </tool>
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