annotate emboss_supermatcher.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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10
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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1 <tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0.1">
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2 <!-- puts file information in output report -->
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3 <description>Match large sequences against one or more other sequences</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <code file="emboss_format_corrector.py" />
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9 <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen $gapopen -gapextend $gapextend -width $width -wordlen $wordlen -outfile '$ofile1' -errorfile '$ofile2' -aformat3
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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10 $out_format1 -auto</command>
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11 <inputs>
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12 <param name="input1" type="data" format="fasta" label="Large sequences" />
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13 <param name="input2" type="data" format="data" label="Sequences to match" />
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14 <param name="gapopen" type="float" value="10.0" label="Gap opening penalty" />
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15 <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" />
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16 <param name="width" type="integer" value="16" label="Alignment width" />
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17 <param name="wordlen" type="integer" value="6" label="Word length for initial matching" />
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18 <param name="out_format1" type="select" label="Output alignment file format">
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19 <option value="simple">Simple (m)</option>
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20 <option value="fasta">FASTA (m)</option>
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21 <option value="msf">MSF (m)</option>
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22 <option value="srs">SRS (m)</option>
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23 <option value="pair">Pair (p)</option>
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24 <option value="markx0">Markx0 (p)</option>
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25 <option value="markx1">Markx1 (p)</option>
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26 <option value="markx2">Markx2 (p)</option>
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27 <option value="markx3">Markx3 (p)</option>
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28 <option value="markx10">Markx10 (p)</option>
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29 <option value="srspair">SRS pair (p)</option>
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30 <option value="score">Score (p)</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="ofile1" format="simple" />
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35 <data name="ofile2" format="supermatcher" />
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36 </outputs>
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37 <!-- <tests>
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38 <test>
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39 <param name="input1" value="2.fasta"/>
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40 <param name="input2" value="1.fasta"/>
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41 <param name="gapopen" value="10.0"/>
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42 <param name="gapextend" value="0.5"/>
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43 <param name="width" value="16"/>
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44 <param name="wordlen" value="6"/>
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45 <param name="out_format1" value="fasta"/>
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46 <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
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47 </test>
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48 </tests> -->
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49 <help>
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50 You can view the original documentation here_.
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51
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52 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/supermatcher.html
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53 </help>
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54 <expand macro="citations" />
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55 </tool>