Mercurial > repos > jay > pdaug_aa_property_based_peptide_generation
annotate PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.xml @ 9:fadecf370cd1 draft default tip
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Wed, 12 Jan 2022 20:40:16 +0000 |
parents | ea405d064794 |
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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"
jay
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3 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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4 <requirements> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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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"
jay
parents:
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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"
jay
parents:
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7 </requirements> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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8 <stdio> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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9 <exit_code range="1" level="fatal" /> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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10 </stdio> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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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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parents:
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13 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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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"
jay
parents:
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15 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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16 #if $SelLibGene.LibGene == 'Random' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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17 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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18 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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19 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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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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parents:
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22 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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23 #if $SelLibGene.LibGene == 'Helices' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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24 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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25 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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26 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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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"
jay
parents:
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29 #if $SelLibGene.LibGene == 'Kinked' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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30 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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31 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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32 --lenmin_s '$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"
jay
parents:
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35 #if $SelLibGene.LibGene == 'Oblique' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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36 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
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37 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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38 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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39 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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40 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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41 #if $SelLibGene.LibGene == 'Centrosymmetric' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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42 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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43 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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44 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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45 #end if |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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46 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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47 #if $SelLibGene.LibGene == 'HelicesACP' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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48 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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49 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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50 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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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"
jay
parents:
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53 #if $SelLibGene.LibGene == 'Hepahelices' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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54 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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55 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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56 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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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 $SelLibGene.LibGene == 'AMPngrams' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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60 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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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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parents:
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64 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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65 #if $SelLibGene.LibGene == 'AmphipathicArc' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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66 --seq_num '$SelLibGene.seq_num' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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67 --lenmax_s '$SelLibGene.lenmax_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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68 --lenmin_s '$SelLibGene.lenmin_s' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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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' |
6
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
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71 #end if |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
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72 |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
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73 |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
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74 #if $SelLibGene.LibGene == 'MixedLibrary' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
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75 --seq_num '$SelLibGene.seq_num' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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76 --centrosymmetric '$SelLibGene.centrosymmetric' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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77 --centroasymmetric '$SelLibGene.centroasymmetric' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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78 --helix '$SelLibGene.helix' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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79 --kinked '$SelLibGene.kinked' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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80 --oblique '$SelLibGene.oblique' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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81 --rand '$SelLibGene.rand' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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82 --randAMP '$SelLibGene.randAMP' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
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83 --randAMPnoCM '$SelLibGene.randAMPnoCM' |
ea405d064794
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
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84 #end if |
0
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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85 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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86 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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87 --OutFasta '$output1' |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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88 |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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89 ]]></command> |
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90 |
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91 |
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92 <inputs> |
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93 |
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94 <conditional name='SelLibGene' > |
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95 |
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96 <param name="LibGene" type="select" label="Methods to generate peptide sequence" argument=""> |
6
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97 <option value="AmphipathicArc">AmphipathicArc Peptides</option> |
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98 <option value="AMPngrams">AMPngrams Peptides</option> |
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99 <option value="Centrosymmetric">Centrosymmetric Peptides</option> |
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100 <option value="Helices">Helices Peptides</option> |
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101 <option value="HelicesACP">HelicesACP Peptides</option> |
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102 <option value="Hepahelices">Hepahelices Peptides</option> |
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103 <option value="Kinked">Kinked Peptides</option> |
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104 <option value="Oblique">Oblique Peptides</option> |
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105 <option value="Random">Random Peptides</option> |
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106 <option value="MixedLibrary">MixedLibrary Peptides</option> |
0
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107 </param> |
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108 |
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109 <when value="Random"> |
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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 <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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114 </when> |
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115 |
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116 <when value="Helices"> |
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117 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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118 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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119 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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120 </when> |
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121 |
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122 <when value="Kinked"> |
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123 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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124 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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125 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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126 </when> |
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127 |
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128 <when value="Oblique"> |
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129 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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130 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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131 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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132 </when> |
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133 |
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134 <when value="Centrosymmetric"> |
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135 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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136 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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137 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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138 <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."> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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139 <option value="asymmetric">asymmetric</option> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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140 <option value="symmetric" >symmetric</option> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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141 </param> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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142 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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143 |
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144 <when value="HelicesACP"> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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145 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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146 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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147 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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148 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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149 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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150 <when value="Hepahelices"> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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151 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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152 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
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153 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
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154 </when> |
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155 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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156 <when value="AMPngrams"> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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157 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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158 <param name="n_min" type="integer" value="3" label="Minimum length" argument="--n_min_s" help="Minimum length of generated peptides." /> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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159 <param name="n_max" type="integer" value="1" label="Maximum length" argument="--n_max_s" help="Maximum length of generated peptides."/> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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160 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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161 |
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162 <when value="AmphipathicArc"> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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163 <param name="seq_num" type="integer" value="5" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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164 <param name="lenmin_s" type="integer" value="7" label="Minimum length" argument="--lenmin_s" help="Minimum length of generated peptides."/> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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165 <param name="lenmax_s" type="integer" value="21" label="Maximum length" argument="--lenmax_s" help="Maximum length of generated peptides."/> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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166 <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."/> |
1199b572b86c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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167 <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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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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168 </when> |
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169 |
6
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170 <when value="MixedLibrary"> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
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171 |
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172 <param name="seq_num" type="integer" value="1000" label="Number of peptides" argument= "--seq_num" help="Number of peptides."/> |
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173 <param name="centrosymmetric" type="integer" value="5" label="Ratio of symmetric centrosymmetric sequences in the library" argument="--lenmin_s" help="Ratio of symmetric centrosymmetric sequences in the library"/> |
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174 <param name="centroasymmetric" type="integer" value="5" label="Ratio of asymmetric centrosymmetric sequences" help="Ratio of asymmetric centrosymmetric sequences in the library"/> |
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175 <param name="helix" type="integer" value="3" label="Ratio of asymmetric centrosymmetric sequences" help="Ratio of asymmetric centrosymmetric sequences in the library"/> |
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176 <param name="kinked" type="integer" value="3" label="Ratio of kinked" help="Ratio of kinked amphipathic helical sequences in the library"/> |
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177 <param name="oblique" type="integer" value="2" label="Ratio of oblique" help="Ratio of oblique oriented amphipathic helical sequences in the library"/> |
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178 <param name="rand" type="integer" value="10" label="Ratio of random sequneces" help="Ratio of random sequneces in the library"/> |
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179 <param name="randAMP" type="integer" value="10" label="Ratio of random sequences with APD2 amino acid distribution" help="Ratio of random sequences with APD2 amino acid distribution in the library"/> |
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180 <param name="randAMPnoCM" type="integer" value="5" label="Ratio of random sequences with APD2 amino acid distribution without Cys and Met in the library" help="Ratio of random sequences with APD2 amino acid distribution in the library"/> |
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181 |
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182 </when> |
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183 |
0
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184 </conditional> |
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185 </inputs> |
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186 |
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187 <outputs> |
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188 <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelLibGene.LibGene} (fasta)" /> |
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189 </outputs> |
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190 |
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191 <tests> |
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192 <test> |
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193 |
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194 <param name="LibGene" value="Random"/> |
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195 <param name="seq_num" value="5" /> |
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196 <param name="lenmin_s" value="7" /> |
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197 <param name="lenmax_s" value="21" /> |
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198 <param name="S_proba" value="1.0" /> |
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199 <output name='output1' file="Out1.fasta" lines_diff='20' /> |
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200 |
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201 </test> |
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202 |
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203 <test> |
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204 |
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205 <param name="LibGene" value="Helices"/> |
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206 <param name="seq_num" value="5" /> |
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207 <param name="lenmin_s" value="7" /> |
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208 <param name="lenmax_s" value="21" /> |
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209 <output name='output1' file="Out2.fasta" lines_diff='20' /> |
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210 |
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211 </test> |
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212 |
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213 <test> |
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214 |
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215 <param name="LibGene" value="Kinked"/> |
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216 <param name="seq_num" value="5" /> |
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217 <param name="lenmin_s" value="7" /> |
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218 <param name="lenmax_s" value="21" /> |
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219 <output name='output1' file="Out3.fasta" lines_diff='20' /> |
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220 |
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221 </test> |
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222 |
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223 <test> |
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224 <param name="LibGene" value="Oblique"/> |
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225 <param name="seq_num" value="5" /> |
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226 <param name="lenmin_s" value="7" /> |
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227 <param name="lenmax_s" value="21" /> |
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228 <output name='output1' file="Out4.fasta" lines_diff='20' /> |
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229 |
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230 </test> |
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231 |
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232 <test> |
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233 |
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234 <param name="LibGene" value="Centrosymmetric"/> |
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235 <param name="seq_num" value="5" /> |
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236 <param name="lenmin_s" value="7" /> |
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237 <param name="lenmax_s" value="21" /> |
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238 <param name="symmetry_s" value="asymmetric" /> |
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239 <output name='output1' file="Out5.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="HelicesACP"/> |
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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 <output name='output1' file="Out6.fasta" lines_diff='20' /> |
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249 |
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250 </test> |
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251 |
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252 <test> |
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253 <param name="LibGene" value="Hepahelices"/> |
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254 <param name="seq_num" value="5" /> |
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255 <param name="lenmin_s" value="7" /> |
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256 <param name="lenmax_s" value="21" /> |
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257 <output name='output1' file="Out7.fasta" lines_diff='20' /> |
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258 |
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259 </test> |
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260 |
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261 <test> |
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262 <param name="LibGene" value="AMPngrams"/> |
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263 <param name="seq_num" value="5" /> |
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264 <param name="lenmin_s" value="7" /> |
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265 <param name="lenmax_s" value="21" /> |
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266 <output name='output1' file="Out8.fasta" lines_diff='20' /> |
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267 |
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268 </test> |
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269 |
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270 <test> |
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271 <param name="LibGene" value="AmphipathicArc"/> |
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272 <param name="seq_num" value="5" /> |
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273 <param name="lenmin_s" value="7" /> |
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274 <param name="lenmax_s" value="21" /> |
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275 <param name="arcsize" value="180" /> |
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276 <param name="hydgra" value="false" /> |
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277 <output name='output1' file="Out9.fasta" lines_diff='20' /> |
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278 |
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279 </test> |
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280 |
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281 </tests> |
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282 |
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283 <help><![CDATA[ |
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284 .. class:: infomark |
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285 |
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286 **What it does** |
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287 |
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288 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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289 |
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290 * **Random** Generates random sequences with a specified amino acid distribution. |
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291 * **Helices** Generate presumed amphipathic helical sequences with a hydrophobic moment. |
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292 * **Kinked** Generates presumed amphipathic helices with a kink (Pro residue). |
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293 * **Oblique** Generates presumed oblique oriented sequences in presence of lipid membranes. |
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294 * **Centrosymmetric** Generates centrosymmetric sequences with a symmetry axis. |
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295 * **AmphipathicArc** Generates presumed amphipathic helices with controlled hydrophobic arc size. |
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296 * **HelicesACP** Generates sequences with the amino acid probability of helical ACPs. |
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297 * **MixedLibrary** Generates a mixed library of sequences of most other classes. |
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298 * **Hepahelices** Generates presumed amphipathic helices with a heparin-binding-domain. |
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299 * **AMPngrams** Generates sequences from most frequent ngrams in the APD3. |
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300 |
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301 ----- |
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302 |
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303 **Inputs** |
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304 **1** Random Peptides |
0
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305 * **--seq_num** Number of sequences to be generated. |
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306 * **--lenmin_s** Peptide minimum legnth. |
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307 * **--lenmax_s** Peptide maximum legnth. |
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308 * **--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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309 |
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310 **2** Helice Peptides |
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311 * **--seq_num** Number of sequence to be generated. |
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312 * **--lenmin_s** Peptide minimum length. |
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313 * **--lenmax_s** Peptide maximum length. |
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314 |
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315 **3** Kinked Peptides |
0
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316 * **--seq_num** Number of sequences to be generated. |
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317 * **--lenmin_s** Peptide minimum length. |
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318 * **--lenmax_s** Peptide maximum length. |
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319 |
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320 **4** Obliqu Peptides |
0
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321 * **--seq_num** Number of sequence to be generated. |
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322 * **--lenmin_s** Peptide minimum length. |
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323 * **--lenmax_s** Peptide maximum length. |
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324 |
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325 **5** Centrosymmetric Peptides |
0
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326 * **--seq_num** Number of sequences to be generated. |
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327 * **--lenmin_s** Peptide minimum length. |
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328 * **--lenmax_s** Peptide maximum length. |
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329 * **--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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330 |
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331 **6** HelicesACP Peptides |
0
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332 * **--seq_num** Number of sequences to be generated. |
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333 * **--lenmin_s** Peptide minimum length. |
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334 * **--lenmax_s** Peptide maximum length. |
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335 |
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336 **7** Hepahelices Peptides |
0
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337 * **--seq_num** Number of sequences to be generated. |
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338 * **--lenmin_s** Peptide minimum length. |
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339 * **--lenmax_s** Peptide maximum length. |
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340 |
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341 **7** AMPngrams Peptides |
0
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342 * **--seq_num** Number of sequence to be generated. |
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343 * **--lenmin_s** Peptide minimum length. |
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344 * **--lenmax_s** Peptide maximum length. |
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345 |
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346 **9** AmphipathicArc Peptides |
0
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347 * **--seq_num** Number of sequence to be generated. |
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348 * **--lenmin_s** Peptide minimum length. |
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349 * **--lenmax_s** Peptide maximum lenngth. |
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350 * **--arcsize** Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture |
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351 |
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352 **10** MixedLibrary Peptides |
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353 * **Todo** |
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354 |
0
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355 ----- |
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356 |
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357 |
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358 **Outputs** |
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359 * Returns fasta files with peptide sequences.]]></help> |
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360 |
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361 |
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362 <citations> |
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363 |
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364 <citation type="bibtex"> |
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365 @misc{PDAUGGITHUB, |
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366 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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367 year = {2020}, |
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368 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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369 publisher = {GitHub}, |
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370 journal = {GitHub repository}, |
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371 url = |
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372 {https://github.com/jaidevjoshi83/pdaug.git}, |
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373 } |
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374 </citation> |
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375 |
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376 <citation type="bibtex"> |
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377 @article{müller_gabernet_hiss_schneider_2017, |
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378 title={modlAMP: Python for antimicrobial peptides}, |
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379 volume={33}, |
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380 DOI={10.1093/bioinformatics/btx285}, |
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381 number={17}, |
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382 journal={Bioinformatics}, |
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383 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, |
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384 year={2017}, |
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385 pages={2753–2755} |
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386 } |
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387 </citation> |
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388 |
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389 </citations> |
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390 |
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391 </tool> |
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392 |
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393 |
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394 |
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395 |
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396 |