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annotate emboss_checktrans.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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11
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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1 <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0.1">
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2 <description>Reports STOP codons and ORF statistics of a protein</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>checktrans -sequence '$input1' -outfile '$out_file1' -outseq '$out_file2' -osformat3 $out_format2 -outfeat '$out_file3' -offormat4 $out_format3 -orfml $orfml -addlast $addlast -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="orfml" type="integer" value="100" label="Minimum ORF length to report" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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12 <param name="addlast" type="select" label="An asterisk in the protein sequence indicates the position of a STOP codon" help="Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <option value="yes">Yes</option>
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14 <option value="no">No</option>
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15 </param>
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16 <param name="out_format2" type="select" label="Output sequence file format">
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17 <option value="fasta">FASTA (m)</option>
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18 <option value="acedb">ACeDB (m)</option>
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19 <option value="asn1">ASN.1 (m)</option>
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20 <option value="clustal">Clustal (m)</option>
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21 <option value="codata">CODATA (m)</option>
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22 <option value="embl">EMBL (m)</option>
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23 <option value="fitch">Fitch (m)</option>
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24 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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25 <option value="genbank">GENBANK (m)</option>
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26 <option value="gff">GFF (m)</option>
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27 <option value="hennig86">Hennig86 (m)</option>
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28 <option value="ig">Intelligenetics (m)</option>
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29 <option value="jackknifer">Jackknifer (m)</option>
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30 <option value="jackknifernon">Jackknifernon (m)</option>
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31 <option value="mega">Mega (m)</option>
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32 <option value="meganon">Meganon (m)</option>
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33 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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34 <option value="pir">NBRF (PIR) (m)</option>
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35 <option value="ncbi">NCBI style FASTA (m)</option>
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36 <option value="nexus">Nexus/PAUP (m)</option>
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37 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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38 <option value="phylip">PHYLIP interleaved (m)</option>
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39 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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40 <option value="selex">SELEX (m)</option>
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41 <option value="staden">Staden (s)</option>
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42 <option value="strider">DNA strider (m)</option>
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43 <option value="swiss">SwisProt entry (m)</option>
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44 <option value="text">Plain sequence (s)</option>
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45 <option value="treecon">Treecon (m)</option>
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46 </param>
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47 <param name="out_format3" type="select" label="Output feature file format">
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48 <option value="gff">GFF</option>
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49 <option value="embl">EMBL</option>
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50 <option value="swiss">SwissProt</option>
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51 </param>
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52 </inputs>
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53 <outputs>
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54 <data name="out_file1" format="checktrans" />
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55 <data name="out_file2" format="fasta" />
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56 <data name="out_file3" format="gff" />
10
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57 </outputs>
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58 <!-- <tests>
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59 <test>
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60 <param name="input1" value="2.fasta"/>
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61 <param name="orfml" value="100"/>
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62 <param name="addlast" value="yes"/>
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63 <param name="out_format2" value="fasta"/>
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64 <param name="out_format3" value="gff"/>
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65 <output name="out_file1" file="emboss_checktrans_out1.txt"/>
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66 <output name="out_file2" file="emboss_checktrans_out2.fasta"/>
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67 <output name="out_file3" file="emboss_checktrans_out3.gff"/>
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68 </test>
11
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69 </tests> -->
10
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70 <help>
11
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71 .. class:: warningmark
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72
11
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73 The input dataset needs to be sequences.
10
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74
11
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75 -----
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76
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77 You can view the original documentation here_.
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78
11
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79 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/checktrans.html
10
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80 </help>
11
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81 <expand macro="citations" />
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9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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82 </tool>