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annotate emboss_biosed.xml @ 13:8992d258e42f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
author iuc
date Fri, 22 Jun 2018 03:24:47 -0400
parents d49956b87f7e
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13
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: biosed4" name="biosed" version="@VERSION@">
10
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2 <description>Replace or delete sequence sections</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>biosed -sequence '$input1' -outseq '$out_file1' -target '$target' -replace '$replace' -osformat2 $out_format1 -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="fasta" label="On query" />
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11 <param name="target" type="text" value="atg" label="Replace all" />
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12 <param name="replace" type="text" value="atg" label="with" />
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13 <param name="out_format1" type="select" label="Output sequence file format">
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14 <option value="fasta">FASTA (m)</option>
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15 <option value="acedb">ACeDB (m)</option>
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16 <option value="asn1">ASN.1 (m)</option>
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17 <option value="clustal">Clustal (m)</option>
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18 <option value="codata">CODATA (m)</option>
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19 <option value="embl">EMBL (m)</option>
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20 <option value="fitch">Fitch (m)</option>
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21 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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22 <option value="genbank">GENBANK (m)</option>
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23 <option value="gff">GFF (m)</option>
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24 <option value="hennig86">Hennig86 (m)</option>
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25 <option value="ig">Intelligenetics (m)</option>
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26 <option value="jackknifer">Jackknifer (m)</option>
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27 <option value="jackknifernon">Jackknifernon (m)</option>
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28 <option value="mega">Mega (m)</option>
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29 <option value="meganon">Meganon (m)</option>
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30 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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31 <option value="pir">NBRF (PIR) (m)</option>
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32 <option value="ncbi">NCBI style FASTA (m)</option>
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33 <option value="nexus">Nexus/PAUP (m)</option>
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34 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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35 <option value="phylip">PHYLIP interleaved (m)</option>
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36 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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37 <option value="selex">SELEX (m)</option>
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38 <option value="staden">Staden (s)</option>
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39 <option value="strider">DNA strider (m)</option>
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40 <option value="swiss">SwisProt entry (m)</option>
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41 <option value="text">Plain sequence (s)</option>
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42 <option value="treecon">Treecon (m)</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <data name="out_file1" format="txt" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input1" value="2.fasta"/>
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51 <param name="target" value="atg"/>
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52 <param name="replace" value="agt"/>
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53 <param name="out_format1" value="fasta"/>
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54 <output name="out_file1" file="emboss_biosed_out.fasta"/>
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55 </test>
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56 </tests>
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57 <help>
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58 .. class:: warningmark
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59
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60 The input dataset needs to be sequences.
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61
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62 -----
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63
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64 You can view the original documentation here_.
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65
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66 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/biosed.html
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67 </help>
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68 <expand macro="citations" />
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69 </tool>