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annotate emboss_water.xml @ 20:21a9fb508031 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:05:39 +0000
parents 27c43fb015f0
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27c43fb015f0 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: water107" name="water" version="@VERSION@.1">
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2 <description>Smith-Waterman local alignment</description>
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21a9fb508031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools" />
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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>water -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -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" />
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13 <param name="gapopen" type="float" value="10.0" label="Gap open penalty" />
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14 <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" />
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15 <param name="brief" type="select" label="Brief identity and similarity">
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16 <option value="yes">Yes</option>
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17 <option value="no">No</option>
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18 </param>
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19 <param name="out_format1" type="select" label="Output alignment file format">
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20 <option value="srs">SRS (m)</option>
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21 <option value="simple">Simple (m)</option>
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22 <option value="fasta">FASTA (m)</option>
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23 <option value="msf">MSF (m)</option>
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24 <option value="pair">Pair (p)</option>
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25 <option value="markx0">Markx0 (p)</option>
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26 <option value="markx1">Markx1 (p)</option>
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27 <option value="markx2">Markx2 (p)</option>
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28 <option value="markx3">Markx3 (p)</option>
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29 <option value="markx10">Markx10 (p)</option>
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30 <option value="srspair">SRS pair (p)</option>
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31 <option value="score">Score (p)</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="out_file1" format="srs" />
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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="brief" value="no"/>
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44 <param name="out_format1" value="score"/>
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45 <output name="out_file1" file="emboss_water_out.score"/>
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46 </test>
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47 </tests>
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48 <help>
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49 .. class:: warningmark
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50
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51 The input datasets need to be sequences.
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52
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53 -----
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54
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55 You can view the original documentation here_.
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56
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57 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/water.html
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58 </help>
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59 <expand macro="citations" />
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60 </tool>