Mercurial > repos > devteam > emboss_5

annotate emboss_est2genome.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: est2genome32" name="est2genome" version="5.0.0.1">
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2 <description>Align EST and genomic DNA sequences</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 <command>est2genome -estsequence '$input1' -genomesequence '$input2' -outfile '$out_file1' -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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8 $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="fasta" label="EST sequence(s)" />
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11 <param name="input2" type="data" format="data" label="Genomic sequence" />
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12 <param name="match" type="integer" value="1" label="Score for matching two bases" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <param name="mismatch" type="integer" value="1" label="Cost for mismatching two bases" />
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14 <param name="gappenalty" type="integer" value="2" label="Cost for deleting a single base in either sequence, excluding introns" />
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15 <param name="intronpenalty" type="integer" value="40" label="Cost for an intron, independent of length" />
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16 <param name="splicepenalty" type="integer" value="20" label="Cost for an intron, independent of length and starting/ending on donor-acceptor sites" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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17 <param name="minscore" type="integer" value="30" label="Exclude alignments with scores below this threshold score" />
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18 <param name="reverse" type="select" label="Reverse the orientation of the EST sequence">
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19 <option value="no">No</option>
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20 <option value="yes">Yes</option>
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21 </param>
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22 <param name="splice" type="select" label="Use donor and acceptor splice sites">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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23 <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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24 <option value="no">No</option>
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25 </param>
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26 <param name="mode" type="select" label="Comparison mode">
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27 <option value="both">Both strands</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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28 <option value="forward">Forward strand only</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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29 <option value="reverse">Reverse strand only</option>
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30 </param>
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31 <param name="best" type="select" label="Only best comparisons">
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32 <option value="yes">Yes</option>
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33 <option value="no">No</option>
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34 </param>
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35 <param name="shuffle" type="integer" value="0" label="Shuffle" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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36 <param name="seed" type="integer" value="20825" label="Random number seed" />
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37 <param name="align" type="select" label="Show the alignment">
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38 <option value="no">No</option>
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39 <option value="yes">Yes</option>
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40 </param>
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41 <param name="width" type="integer" value="50" label="Alignment width" />
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42 </inputs>
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43 <outputs>
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44 <data name="out_file1" format="est2genome" />
10
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input1" value="2.fasta"/>
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49 <param name="input2" value="1.fasta"/>
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50 <param name="match" value="1"/>
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51 <param name="mismatch" value="1"/>
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52 <param name="match" value="1"/>
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53 <param name="gappenalty" value="2"/>
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54 <param name="intronpenalty" value="40"/>
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55 <param name="splicepenalty" value="20"/>
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56 <param name="minscore" value="30"/>
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57 <param name="reverse" value="no"/>
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58 <param name="splice" value="yes"/>
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59 <param name="mode" value="both"/>
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60 <param name="best" value="yes"/>
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61 <param name="shuffle" value="0"/>
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62 <param name="seed" value="20825"/>
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63 <param name="align" value="no"/>
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64 <param name="width" value="50"/>
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65 <output name="out_file1" file="emboss_est2genome_out.est2genome"/>
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66 </test>
11
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67 </tests>
10
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68 <help>
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69 .. class:: warningmark
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70
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71 The input dataset needs to be sequences.
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72
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73 -----
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74
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75 You can view the original documentation here_.
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76
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77 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/est2genome.html
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78 </help>
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79 <expand macro="citations" />
10
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80 </tool>