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annotate emboss_extractfeat.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: extractfeat34" name="extractfeat" version="@VERSION@.1">
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2 <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->
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3 <description>Extract features from a sequence</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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4 <expand macro="bio_tools" />
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <code file="emboss_format_corrector.py" />
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10 <command>extractfeat -sequence '$input1' -outseq '$out_file1' -before $before -after $after -source '$source' -type '$type' -sense $sense -minscore $minscore -maxscore $maxscore -tag '$tag' -value
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11 '$value' -join $join -featinname $featinname -describe '$describe' -osformat2 $out_format1 -auto</command>
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12 <inputs>
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13 <param name="input1" type="data" format="data" label="Sequences" />
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14 <param name="before" type="integer" value="0" label="Number of bases or residues before the feature to include in the extracted sequence" />
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15 <param name="after" type="integer" value="0" label="Number of bases or residues after the feature to include in the extracted sequence" />
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16 <param name="source" type="text" value="*" label="Feature source" />
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17 <param name="type" type="text" value="*" label="Feature type" />
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18 <param name="sense" type="select" label="Feature sense">
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19 <option value="0">Any sense</option>
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20 <option value="1">Forward sense</option>
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21 <option value="-1">Reverse sense</option>
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22 </param>
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23 <param name="minscore" type="float" value="0.0" label="Minimum score" />
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24 <param name="maxscore" type="float" value="0.0" label="Maximum score" />
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25 <param name="tag" type="text" value="*" label="Feature tags" />
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26 <param name="value" type="text" value="*" label="Tag values" />
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27 <param name="join" type="select" label="Join features">
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28 <option value="no">No</option>
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29 <option value="yes">Yes</option>
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30 </param>
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31 <param name="featinname" type="select" label="Put feature type in sequence name">
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32 <option value="no">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 <param name="describe" type="text" value="" label="Specify one or more tag names that should be added to the output sequence Description text" />
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36 <param name="out_format1" type="select" label="Output sequence file format">
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37 <option value="fasta">FASTA (m)</option>
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38 <option value="acedb">ACeDB (m)</option>
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39 <option value="asn1">ASN.1 (m)</option>
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40 <option value="clustal">Clustal (m)</option>
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41 <option value="codata">CODATA (m)</option>
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42 <option value="embl">EMBL (m)</option>
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43 <option value="fitch">Fitch (m)</option>
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44 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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45 <option value="genbank">GENBANK (m)</option>
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46 <option value="gff">GFF (m)</option>
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47 <option value="hennig86">Hennig86 (m)</option>
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48 <option value="ig">Intelligenetics (m)</option>
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49 <option value="jackknifer">Jackknifer (m)</option>
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50 <option value="jackknifernon">Jackknifernon (m)</option>
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51 <option value="mega">Mega (m)</option>
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52 <option value="meganon">Meganon (m)</option>
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53 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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54 <option value="pir">NBRF (PIR) (m)</option>
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55 <option value="ncbi">NCBI style FASTA (m)</option>
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56 <option value="nexus">Nexus/PAUP (m)</option>
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57 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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58 <option value="phylip">PHYLIP interleaved (m)</option>
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59 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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60 <option value="selex">SELEX (m)</option>
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61 <option value="staden">Staden (s)</option>
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62 <option value="strider">DNA strider (m)</option>
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63 <option value="swiss">SwisProt entry (m)</option>
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64 <option value="text">Plain sequence (s)</option>
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65 <option value="treecon">Treecon (m)</option>
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66 </param>
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67 </inputs>
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68 <outputs>
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69 <data name="out_file1" format="fasta" />
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70 </outputs>
10
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71 <help>
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72 You can view the original documentation here_.
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73
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74 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/extractfeat.html
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75 </help>
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76 <expand macro="citations" />
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77 </tool>