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annotate emboss_fuzznuc.xml @ 13:d5c3794bd246 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
author iuc
date Mon, 23 Apr 2018 13:04:47 -0400
parents 0e2484b6829b
children d0847fe9b443
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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: fuzznuc37" name="fuzznuc" version="5.0.2">
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2 <description>Nucleic acid pattern search</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>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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9 <inputs>
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10 <param name="input1" type="data" format="fasta" label="Sequences" />
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11 <param name="pattern" type="text" value="" label="Search pattern">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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12 <sanitizer>
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13 <valid initial="string.printable">
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14 <remove value="&apos;"/>
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15 </valid>
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16 <mapping initial="none">
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17 <add source="&apos;" target=""/>
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18 </mapping>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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19 </sanitizer>
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20 </param>
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21 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
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22 <param name="complement" type="select" label="Search complementary strand">
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23 <option value="no">No</option>
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24 <option value="yes">Yes</option>
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25 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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26 <param name="out_format1" type="select" label="Output report file format">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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27 <option value="seqtable">SeqTable</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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28 <option value="embl">EMBL</option>
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29 <option value="genbank">GENBANK</option>
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>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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31 <option value="pir">PIR</option>
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32 <option value="swiss">SwissProt</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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33 <option value="dbmotif">DbMotif</option>
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34 <option value="diffseq">Diffseq</option>
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35 <option value="excel">Excel (tab delimited)</option>
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36 <option value="feattable">FeatTable</option>
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37 <option value="motif">Motif</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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38 <option value="regions">Regions</option>
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39 <option value="simple">SRS Simple</option>
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40 <option value="fuzznuc">Fuzznuc Output File</option>
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41 <option value="srs">SRS</option>
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42 <option value="table">Table</option>
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43 <option value="tagseq">TagSeq</option>
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44 </param>
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45 </inputs>
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46 <outputs>
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47 <data name="out_file1" format="fuzznuc" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="input1" value="2.fasta"/>
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52 <param name="pattern" value="AA"/>
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53 <param name="mismatch" value="0"/>
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54 <param name="complement" value="no"/>
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55 <param name="out_format1" value="excel"/>
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56 <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
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57 </test>
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58 </tests>
10
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59 <help>
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60 .. class:: warningmark
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61
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62 The input dataset needs to be sequences.
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63
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64 -----
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65
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66 You can view the original documentation here_.
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67
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68 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html
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69 </help>
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70 <expand macro="citations" />
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71 </tool>