annotate emboss_equicktandem.xml @ 18:63dd26468588 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"
author iuc
date Fri, 09 Jul 2021 18:36:34 +0000
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8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: equicktandem31" name="equicktandem" version="@VERSION@.1">
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2 <description>Finds tandem repeats</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>equicktandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -maxrepeat $maxrepeat -threshold $threshold -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="maxrepeat" type="integer" value="600" label="Maximum repeat size" />
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12 <param name="threshold" type="integer" value="20" label="Threshold score" />
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13 <param name="out_format1" type="select" label="Output report file format">
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14 <option value="table">Table</option>
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15 <option value="embl">EMBL</option>
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16 <option value="genbank">GENBANK</option>
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17 <option value="gff">GFF</option>
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18 <option value="pir">PIR</option>
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19 <option value="swiss">SwissProt</option>
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20 <option value="dbmotif">DbMotif</option>
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21 <option value="diffseq">Diffseq</option>
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22 <option value="excel">Excel (tab delimited)</option>
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23 <option value="feattable">FeatTable</option>
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24 <option value="motif">Motif</option>
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25 <option value="regions">Regions</option>
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26 <option value="seqtable">SeqTable</option>
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27 <option value="simple">SRS Simple</option>
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28 <option value="srs">SRS</option>
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29 <option value="tagseq">TagSeq</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data name="out_file1" format="table" />
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34 <data name="ofile2" format="equicktandem" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input1" value="1.fasta"/>
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39 <param name="maxrepeat" value="600"/>
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40 <param name="threshold" value="20"/>
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41 <param name="out_format1" value="table"/>
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42 <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
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43 </test>
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44 </tests>
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45 <help>
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46 .. class:: warningmark
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47
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48 The input dataset needs to be sequences.
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49
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50 -----
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51
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52 You can view the original documentation here_.
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53
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54 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/equicktandem.html
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55 </help>
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56 <expand macro="citations" />
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57 </tool>