Mercurial > repos > devteam > emboss_5

annotate emboss_coderet.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
children
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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: coderet13" name="coderet" version="@VERSION@">
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2 <description>Extract CDS, mRNA and translations from feature tables</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>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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>coderet -seqall '$input1' -outfile '$out_file1' -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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10 <command>coderet -seqall '$input1' -outfile '$out_file1' -auto</command>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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11 <inputs>
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12 <param name="input1" type="data" format="data" label="On query" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <!--
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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14 <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Extract CDS sequences" />
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15 <param name="mrna" type="select" label="Extract mRNA sequences">
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16 <option value="yes">Yes</option>
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17 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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18 </param>
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iuc
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19 <param name="translation" type="select" label="Extract translated sequences">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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20 <option value="yes">Yes</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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21 <option value="no">No</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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22 </param>
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23 <param name="out_format1" type="select" label="Output sequence file format">
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24 <option value="fasta">FASTA (m)</option>
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25 <option value="acedb">ACeDB (m)</option>
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26 <option value="asn1">ASN.1 (m)</option>
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27 <option value="clustal">Clustal (m)</option>
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28 <option value="codata">CODATA (m)</option>
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29 <option value="embl">EMBL (m)</option>
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30 <option value="fitch">Fitch (m)</option>
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31 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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32 <option value="genbank">GENBANK (m)</option>
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33 <option value="gff">GFF (m)</option>
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34 <option value="hennig86">Hennig86 (m)</option>
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35 <option value="ig">Intelligenetics (m)</option>
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36 <option value="jackknifer">Jackknifer (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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37 <option value="jackknifernon">Jackknifernon (m)</option>
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38 <option value="mega">Mega (m)</option>
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39 <option value="meganon">Meganon (m)</option>
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40 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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41 <option value="pir">NBRF (PIR) (m)</option>
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42 <option value="ncbi">NCBI style FASTA (m)</option>
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43 <option value="nexus">Nexus/PAUP (m)</option>
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44 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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45 <option value="phylip">PHYLIP interleaved (m)</option>
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46 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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47 <option value="selex">SELEX (m)</option>
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48 <option value="staden">Staden (s)</option>
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49 <option value="strider">DNA strider (m)</option>
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50 <option value="swiss">SwisProt entry (m)</option>
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51 <option value="text">Plain sequence (s)</option>
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52 <option value="treecon">Treecon (m)</option>
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53 </param>
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54 -->
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55 </inputs>
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56 <outputs>
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57 <data name="out_file1" format="coderet" />
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58 </outputs>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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59 <tests>
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60 <test>
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61 <param name="input1" value="2.fasta"/>
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62 <output name="out_file1" file="emboss_coderet_out.coderet"/>
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63 </test>
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64 </tests>
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65 <help>
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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/coderet.html
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69 </help>
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70 <expand macro="citations" />
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71 </tool>