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annotate emboss_wordmatch.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: wordmatch110" name="wordmatch" version="5.0.0.1">
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2 <description>Finds all exact matches of a given size between 2 sequences</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>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -aformat3 $out_format1 -offormat4 $out_format2
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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9 -offormat5 $out_format3 -auto</command>
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10 <inputs>
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11 <param name="input1" type="data" format="fasta" label="Sequence 1" />
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12 <param name="input2" type="data" format="fasta" label="Sequence 2" />
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="wordsize" type="integer" value="4" label="Word size" />
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14 <param name="out_format1" type="select" label="Output alignment file format">
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15 <option value="match">Match (m)</option>
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16 <option value="simple">Simple (m)</option>
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17 <option value="fasta">FASTA (m)</option>
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18 <option value="msf">MSF (m)</option>
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19 <option value="srs">SRS (m)</option>
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20 <option value="pair">Pair (p)</option>
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21 <option value="markx0">Markx0 (p)</option>
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22 <option value="markx1">Markx1 (p)</option>
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23 <option value="markx2">Markx2 (p)</option>
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24 <option value="markx3">Markx3 (p)</option>
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25 <option value="markx10">Markx10 (p)</option>
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26 <option value="srspair">SRS pair (p)</option>
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27 <option value="score">Score (p)</option>
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28 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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29 <param name="out_format2" type="select" label="Output feature 1 file format">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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30 <option value="gff">GFF</option>
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31 <option value="embl">EMBL</option>
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32 <option value="swiss">SwissProt</option>
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33 </param>
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34 <param name="out_format3" type="select" label="Output feature 2 file format">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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35 <option value="gff">GFF</option>
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36 <option value="embl">EMBL</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="swiss">SwissProt</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="out_file1" format="match" />
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42 <data name="out_file2" format="gff" />
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43 <data name="out_file3" format="gff" />
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="2.fasta"/>
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48 <param name="input2" value="1.fasta"/>
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49 <param name="wordsize" value="4"/>
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50 <param name="out_format1" value="fasta"/>
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51 <param name="out_format2" value="gff"/>
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52 <param name="out_format3" value="gff"/>
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53 <output name="ofile2" file="emboss_wordmatch_out.embl"/>
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54 </test>
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55 </tests> test takes a long time to run-->
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56 <help>
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57 .. class:: warningmark
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58
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59 The input datasets need to be sequences.
10
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60
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61 -----
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62
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63 You can view the original documentation here_.
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64
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65 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wordmatch.html
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66 </help>
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67 <expand macro="citations" />
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68 </tool>