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annotate emboss_etandem.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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11
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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1 <tool id="EMBOSS: etandem33" name="etandem" version="5.0.0.1">
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2 <description>Looks for tandem repeats in a nucleotide sequence</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <code file="emboss_format_corrector.py" />
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8 <command>etandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="fasta" label="Sequence" />
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11 <param name="minrepeat" type="integer" value="10" label="Minimum repeat size" />
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12 <param name="maxrepeat" type="integer" value="10" label="Maximum repeat size" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <param name="threshold" type="integer" value="20" label="Threshold score" />
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14 <param name="mismatch" type="select" label="Allow N as a mismatch">
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15 <option value="no">No</option>
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16 <option value="yes">Yes</option>
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17 </param>
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18 <param name="uniform" type="select" label="Allow uniform consensus">
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19 <option value="no">No</option>
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20 <option value="yes">Yes</option>
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21 </param>
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22 <param name="out_format1" type="select" label="Output report file format">
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23 <option value="table">Table</option>
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24 <option value="embl">EMBL</option>
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25 <option value="genbank">GENBANK</option>
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26 <option value="gff">GFF</option>
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27 <option value="pir">PIR</option>
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28 <option value="swiss">SwissProt</option>
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29 <option value="dbmotif">DbMotif</option>
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30 <option value="diffseq">Diffseq</option>
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31 <option value="excel">Excel (tab delimited)</option>
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32 <option value="feattable">FeatTable</option>
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33 <option value="motif">Motif</option>
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34 <option value="regions">Regions</option>
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35 <option value="seqtable">SeqTable</option>
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36 <option value="simple">SRS Simple</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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37 <option value="srs">SRS</option>
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38 <option value="tagseq">TagSeq</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="out_file1" format="etandem" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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43 <data name="ofile2" format="table" />
10
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input1" value="1.fasta"/>
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48 <param name="minrepeat" value="10"/>
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49 <param name="maxrepeat" value="10"/>
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50 <param name="threshold" value="20"/>
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51 <param name="mismatch" value="no"/>
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52 <param name="uniform" value="no"/>
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53 <param name="out_format1" value="table"/>
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54 <output name="ofile2" file="emboss_etandem_out.table"/>
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55 </test>
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56 </tests>
10
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57 <help>
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58 .. class:: warningmark
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59
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60 The input dataset needs to be sequences.
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61
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62 -----
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63
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64 You can view the original documentation here_.
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65
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66 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/etandem.html
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67 </help>
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68 <expand macro="citations" />
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69 </tool>