Mercurial > repos > jay > pdaug_aa_property_based_peptide_generation
annotate PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.xml @ 4:8a524069287d draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
author | jay |
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date | Tue, 12 Jan 2021 20:03:25 +0000 |
parents | 1199b572b86c |
children | ea405d064794 |
rev | line source |
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0
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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1 <tool id="pdaug_aa_property_based_peptide_generation" name="PDAUG AA Property Based Peptide Generation" version="0.1.0"> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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2 <description>Generates peptide sequence library based on amino acid properties</description> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 <requirements> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 <requirement type="package" version="0.24.2">pandas</requirement> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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6 <requirement type="package" version="4.1.2">modlamp</requirement> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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7 </requirements> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 <stdio> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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9 <exit_code range="1" level="fatal" /> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10 </stdio> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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11 <command detect_errors="exit_code"><![CDATA[ |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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12 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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13 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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14 python '$__tool_directory__/PDAUG_AA_Property_Based_Peptide_Generation.py' '$SelLibGene.LibGene' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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15 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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16 #if $SelLibGene.LibGene == 'Random' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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17 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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18 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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19 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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20 --S_proba '$SelLibGene.S_proba' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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21 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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22 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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23 #if $SelLibGene.LibGene == 'Helices' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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24 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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25 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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26 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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27 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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29 #if $SelLibGene.LibGene == 'Kinked' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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30 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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31 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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32 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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33 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 #if $SelLibGene.LibGene == 'Oblique' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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37 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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38 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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39 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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40 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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41 #if $SelLibGene.LibGene == 'Centrosymmetric' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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42 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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43 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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44 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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45 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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46 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 #if $SelLibGene.LibGene == 'HelicesACP' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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49 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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50 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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51 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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52 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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53 #if $SelLibGene.LibGene == 'Hepahelices' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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54 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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55 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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56 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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57 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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58 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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59 #if $SelLibGene.LibGene == 'AMPngrams' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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60 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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61 --n_min '$SelLibGene.n_max' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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62 --n_max '$SelLibGene.n_min' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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63 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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64 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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65 #if $SelLibGene.LibGene == 'AmphipathicArc' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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66 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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67 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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68 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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69 --arcsize '$SelLibGene.arcsize' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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70 --hyd_gra '$SelLibGene.hydgra' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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71 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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72 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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73 |
1199b572b86c
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74 --OutFasta '$output1' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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75 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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76 ]]></command> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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77 |
1199b572b86c
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78 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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79 <inputs> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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80 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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81 <conditional name='SelLibGene' > |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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82 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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83 <param name="LibGene" type="select" label="Methods to generate peptide sequence" argument=""> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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84 <option value="Random">Random sequences</option> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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85 <option value="Helices">Presumed amphipathic helical sequences with a hydrophobic moment</option> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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86 <option value="Kinked">Presumed amphipathic helices with a kink (Pro residue)</option> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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87 <option value="Oblique">Presumed oblique oriented sequences in presence of libid membranes</option> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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88 <option value="Centrosymmetric">Centrosymmetric sequences with a symmetry axis</option> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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89 <option value="HelicesACP">Sequences with the amino acid probabiliy of helical ACPs</option> |
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90 <option value="Hepahelices">Presumed amphipathic helices with a heparin-binding-domain</option> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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91 <option value="AMPngrams">Sequences from most frequent ngrams in the APD3</option> |
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92 <option value="AmphipathicArc">Presumed amphipathic helices with controlled hydrophobic arc size</option> |
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93 |
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94 </param> |
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95 |
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96 <when value="Random"> |
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97 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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98 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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99 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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100 <param name="S_proba" type="float" value="1.0" label="Probability" argument="--S_proba" help="AA probability to be used to generate sequences." /> |
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101 </when> |
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102 |
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103 <when value="Helices"> |
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104 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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105 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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106 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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107 </when> |
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108 |
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109 <when value="Kinked"> |
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110 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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111 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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112 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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113 </when> |
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114 |
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115 <when value="Oblique"> |
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116 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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117 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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118 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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119 </when> |
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120 |
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121 <when value="Centrosymmetric"> |
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122 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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123 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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124 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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125 <param name="symmetry_s" type="select" label="Symmetry" argument="--symmetry_s" help="Type of centrosymmetric sequences. symmetric: builds sequences out of only one block, asymmetric: builds sequences out of different blocks."> |
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126 <option value="asymmetric">asymmetric</option> |
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127 <option value="symmetric" >symmetric</option> |
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128 </param> |
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129 </when> |
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130 |
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131 <when value="HelicesACP"> |
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132 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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133 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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134 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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135 </when> |
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136 |
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137 <when value="Hepahelices"> |
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138 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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139 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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140 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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141 </when> |
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142 |
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143 <when value="AMPngrams"> |
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144 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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145 <param name="n_min" type="integer" value="3" label="Minimum length" argument="--n_min_s" help="Minimum length of generated peptides." /> |
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146 <param name="n_max" type="integer" value="1" label="Maximum length" argument="--n_max_s" help="Maximum length of generated peptides."/> |
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147 </when> |
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148 |
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149 <when value="AmphipathicArc"> |
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150 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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151 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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152 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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153 <param name="arcsize" type="integer" value="180" label="Arc size" argument="--arcsize" help="Arc size to choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture."/> |
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154 <param name="hydgra" type="boolean" value="false" argument="--hyd_gra" label="Hydrophobic gradient" help="Method to mutate the generated sequences to have a hydrophobic gradient by substituting the last third of the sequence amino acids to hydrophobic."/> |
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155 </when> |
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156 |
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157 </conditional> |
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158 </inputs> |
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159 |
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160 <outputs> |
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161 <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelLibGene.LibGene} (fasta)" /> |
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162 </outputs> |
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163 |
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164 <tests> |
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165 <test> |
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166 |
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167 <param name="LibGene" value="Random"/> |
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168 <param name="seq_num" value="5" /> |
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169 <param name="lenmin_s" value="7" /> |
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170 <param name="lenmax_s" value="21" /> |
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171 <param name="S_proba" value="1.0" /> |
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172 <output name='output1' file="Out1.fasta" lines_diff='20' /> |
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173 |
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174 </test> |
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175 |
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176 <test> |
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177 |
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178 <param name="LibGene" value="Helices"/> |
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179 <param name="seq_num" value="5" /> |
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180 <param name="lenmin_s" value="7" /> |
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181 <param name="lenmax_s" value="21" /> |
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182 <output name='output1' file="Out2.fasta" lines_diff='20' /> |
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183 |
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184 </test> |
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185 |
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186 <test> |
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187 |
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188 <param name="LibGene" value="Kinked"/> |
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189 <param name="seq_num" value="5" /> |
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190 <param name="lenmin_s" value="7" /> |
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191 <param name="lenmax_s" value="21" /> |
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192 <output name='output1' file="Out3.fasta" lines_diff='20' /> |
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193 |
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194 </test> |
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195 |
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196 <test> |
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197 <param name="LibGene" value="Oblique"/> |
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198 <param name="seq_num" value="5" /> |
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199 <param name="lenmin_s" value="7" /> |
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200 <param name="lenmax_s" value="21" /> |
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201 <output name='output1' file="Out4.fasta" lines_diff='20' /> |
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202 |
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203 </test> |
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204 |
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205 <test> |
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206 |
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207 <param name="LibGene" value="Centrosymmetric"/> |
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208 <param name="seq_num" value="5" /> |
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209 <param name="lenmin_s" value="7" /> |
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210 <param name="lenmax_s" value="21" /> |
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211 <param name="symmetry_s" value="asymmetric" /> |
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212 <output name='output1' file="Out5.fasta" lines_diff='20' /> |
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213 |
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214 </test> |
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215 |
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216 <test> |
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217 <param name="LibGene" value="HelicesACP"/> |
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218 <param name="seq_num" value="5" /> |
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219 <param name="lenmin_s" value="7" /> |
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220 <param name="lenmax_s" value="21" /> |
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221 <output name='output1' file="Out6.fasta" lines_diff='20' /> |
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222 |
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223 </test> |
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224 |
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225 <test> |
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226 <param name="LibGene" value="Hepahelices"/> |
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227 <param name="seq_num" value="5" /> |
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228 <param name="lenmin_s" value="7" /> |
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229 <param name="lenmax_s" value="21" /> |
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230 <output name='output1' file="Out7.fasta" lines_diff='20' /> |
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231 |
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232 </test> |
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233 |
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234 <test> |
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235 <param name="LibGene" value="AMPngrams"/> |
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236 <param name="seq_num" value="5" /> |
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237 <param name="lenmin_s" value="7" /> |
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238 <param name="lenmax_s" value="21" /> |
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239 <output name='output1' file="Out8.fasta" lines_diff='20' /> |
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240 |
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241 </test> |
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242 |
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243 <test> |
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244 <param name="LibGene" value="AmphipathicArc"/> |
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245 <param name="seq_num" value="5" /> |
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246 <param name="lenmin_s" value="7" /> |
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247 <param name="lenmax_s" value="21" /> |
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248 <param name="arcsize" value="180" /> |
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249 <param name="hydgra" value="false" /> |
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250 <output name='output1' file="Out9.fasta" lines_diff='20' /> |
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251 |
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252 </test> |
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253 |
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254 </tests> |
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255 |
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256 <help><![CDATA[ |
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257 .. class:: infomark |
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258 |
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259 **What it does** |
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260 |
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261 This module incorporates different classes to generate peptide sequences with different characteristics from scratch. The following classes are available Random, Helices, Kinked, Oblique, Centrosymmetric, AmphipathicArc, HelicesACP, MixedLibrary, Hepahelices, and AMPngrams. |
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262 |
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263 * **Random** Generates random sequences with a specified amino acid distribution. |
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264 * **Helices** Generate presumed amphipathic helical sequences with a hydrophobic moment. |
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265 * **Kinked** Generates presumed amphipathic helices with a kink (Pro residue). |
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266 * **Oblique** Generates presumed oblique oriented sequences in presence of lipid membranes. |
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267 * **Centrosymmetric** Generates centrosymmetric sequences with a symmetry axis. |
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268 * **AmphipathicArc** Generates presumed amphipathic helices with controlled hydrophobic arc size. |
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269 * **HelicesACP** Generates sequences with the amino acid probability of helical ACPs. |
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270 * **MixedLibrary** Generates a mixed library of sequences of most other classes. |
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271 * **Hepahelices** Generates presumed amphipathic helices with a heparin-binding-domain. |
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272 * **AMPngrams** Generates sequences from most frequent ngrams in the APD3. |
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273 |
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274 ----- |
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275 |
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276 **Inputs** |
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277 **1** Random |
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278 * **--seq_num** Number of sequences to be generated. |
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279 * **--lenmin_s** Peptide minimum legnth. |
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280 * **--lenmax_s** Peptide maximum legnth. |
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281 * **--S_proba** AA probability to be used to generate sequences. Available from str: AMP, AMPnoCM, rand, randnoCM. You can also provide your own list of porbabilities as a list (in AA order, length 20, sum to 1) |
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282 |
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283 **2** Helice |
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284 * **--seq_num** Number of sequence to be generated. |
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285 * **--lenmin_s** Peptide minimum length. |
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286 * **--lenmax_s** Peptide maximum length. |
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287 |
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288 **3** Kinked |
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289 * **--seq_num** Number of sequences to be generated. |
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290 * **--lenmin_s** Peptide minimum length. |
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291 * **--lenmax_s** Peptide maximum length. |
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292 |
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293 **4** Obliqu |
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294 * **--seq_num** Number of sequence to be generated. |
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295 * **--lenmin_s** Peptide minimum length. |
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296 * **--lenmax_s** Peptide maximum length. |
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297 |
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298 **5** Centrosymmetric |
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299 * **--seq_num** Number of sequences to be generated. |
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300 * **--lenmin_s** Peptide minimum length. |
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301 * **--lenmax_s** Peptide maximum length. |
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302 * **--symmetry_s** symmetry type of centrosymmetric sequences. symmetric: builds sequences out of only one block, asymmetric: builds sequences out of different blocks |
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303 |
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304 **6** HelicesACP |
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305 * **--seq_num** Number of sequences to be generated. |
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306 * **--lenmin_s** Peptide minimum length. |
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307 * **--lenmax_s** Peptide maximum length. |
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308 |
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309 **7** Hepahelices |
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310 * **--seq_num** Number of sequences to be generated. |
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311 * **--lenmin_s** Peptide minimum length. |
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312 * **--lenmax_s** Peptide maximum length. |
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313 |
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314 **7** AMPngrams |
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315 * **--seq_num** Number of sequence to be generated. |
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316 * **--lenmin_s** Peptide minimum length. |
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317 * **--lenmax_s** Peptide maximum length. |
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318 |
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319 **9** AmphipathicArc |
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320 * **--seq_num** Number of sequence to be generated. |
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321 * **--lenmin_s** Peptide minimum length. |
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322 * **--lenmax_s** Peptide maximum lenngth. |
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323 * **--arcsize** Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture |
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324 |
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325 ----- |
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326 |
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327 |
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328 **Outputs** |
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329 * Returns fasta files with peptide sequences.]]></help> |
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330 |
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331 |
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332 <citations> |
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333 |
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334 <citation type="bibtex"> |
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335 @misc{PDAUGGITHUB, |
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336 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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337 year = {2020}, |
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338 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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339 publisher = {GitHub}, |
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340 journal = {GitHub repository}, |
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341 url = |
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342 {https://github.com/jaidevjoshi83/pdaug.git}, |
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343 } |
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344 </citation> |
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345 |
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346 <citation type="bibtex"> |
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347 @article{müller_gabernet_hiss_schneider_2017, |
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348 title={modlAMP: Python for antimicrobial peptides}, |
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349 volume={33}, |
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350 DOI={10.1093/bioinformatics/btx285}, |
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351 number={17}, |
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352 journal={Bioinformatics}, |
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353 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, |
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354 year={2017}, |
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355 pages={2753–2755} |
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356 } |
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357 </citation> |
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358 |
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359 </citations> |
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360 |
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361 </tool> |
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362 |
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363 |
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364 |
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365 |
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366 |