Mercurial > repos > jay > pdaug_peptide_core_functions
annotate PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml @ 1:562dc0806625 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
author | jay |
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date | Tue, 29 Dec 2020 04:19:19 +0000 |
parents | e743e76b8991 |
children | 6822d43a5f84 |
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0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 <tool id="pdaug_peptide_core_functions" name="PDAUG Peptide Core Functions" version="0.1.0"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 <description> Peptide sequence related core functions </description> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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3 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 <requirements> |
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"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> |
e743e76b8991
"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> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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7 </requirements> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 <stdio> |
e743e76b8991
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9 <exit_code range="1" level="fatal" /> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10 </stdio> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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11 <command detect_errors="exit_code"><![CDATA[ |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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12 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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14 python '$__tool_directory__/PDAUG_Peptide_Core_Functions.py' '$SelCoreFunction.CoreFunction' |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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16 --InFile '$InFile' |
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17 |
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18 #if $SelCoreFunction.CoreFunction == 'mutateAA' |
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19 --nr '$SelCoreFunction.nr' |
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20 --Prob '$SelCoreFunction.prob' |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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21 #end if |
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22 |
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23 #if $SelCoreFunction.CoreFunction == 'filteraa' |
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24 --FilterAA '$SelCoreFunction.FilterAA' |
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25 #end if |
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26 |
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27 --FastOut '$output1' |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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28 |
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29 ]]></command> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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30 |
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31 <inputs> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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32 |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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33 <param name="InFile" type="data" format="fasta" label="Input file" argument= "--InFile" help="Input fasta file with peptides"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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34 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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35 <conditional name='SelCoreFunction' > |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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36 |
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37 <param name="CoreFunction" type="select" label="Analysis options" argument=""> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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38 <option value="mutateAA">Mutate Amino Acid</option> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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39 <option value="filterduplicates">Filter Duplicates</option> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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40 <option value="keepnaturalaa">Keep Naturalaa</option> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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41 <option value="filteraa">Filter Amino Acid</option> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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42 </param> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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43 |
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44 <when value="mutateAA"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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45 <param name="nr" type="integer" label="Number of mutations" value="3" argument="--nr" help="Number of mutations"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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46 <param name="prob" type="float" label="Probability" value="1.0" argument="--Prob" help="Probability of mutating a sequence" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 </when> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 |
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49 <when value="filterduplicates"> |
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50 </when> |
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51 |
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52 <when value="keepnaturalaa"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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53 </when> |
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54 |
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55 <when value="filteraa"> |
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56 <param name="FilterAA" type="text" value="eisenberg" label="Filter AA" argument="--FilterAA" help="Amino acids to be filtered" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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57 </when> |
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58 |
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59 </conditional> |
e743e76b8991
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60 </inputs> |
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61 |
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62 <outputs> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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63 <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelCoreFunction.CoreFunction} (fasta)" /> |
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64 </outputs> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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65 <tests> |
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66 <test> |
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67 <param name="InFile" value="test1.fasta"/> |
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68 <param name="CoreFunction" value="mutateAA" /> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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69 <param name="nr" value="3"/> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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70 <param name="prob" value="1.0"/> |
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71 <output name="output1" file="out1.fasta" lines_diff="2"/> |
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72 </test> |
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73 <test> |
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74 <param name="InFile" value="test2.fasta"/> |
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75 <param name="CoreFunction" value="filterduplicates" /> |
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76 <output name="output1" file="out2.fasta" /> |
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77 </test> |
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78 <test> |
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79 <param name="InFile" value="test3.fasta"/> |
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80 <param name="CoreFunction" value="keepnaturalaa" /> |
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81 <output name="output1" file="out3.fasta" /> |
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82 </test> |
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83 <test> |
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84 <param name="InFile" value="test4.fasta"/> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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85 <param name="CoreFunction" value="filteraa" /> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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86 <param name="FilterAA" value="eisenberg" /> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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87 <output name="output1" file="out4.fasta" /> |
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88 </test> |
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89 </tests> |
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90 <help><![CDATA[ |
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91 .. class:: infomark |
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92 |
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93 **What it does** |
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94 |
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95 This tool performs some core functions on the peptide sequences and equipped with various options |
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96 |
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97 * **Mutated Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly. |
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98 * **Filter Duplicates** Method to filter duplicates in the sequences from the class attribute sequences. |
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99 * **Keep Naturalaa** Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character. |
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100 * **Filter Amino Acid** Method to filter out corresponding names and descriptor values of sequences with given amino acids in the argument list aminoacids. |
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101 |
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102 ----- |
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103 |
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104 **Inputs** |
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105 |
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106 1 **Mutate Amino Acid** |
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107 * **--InFile** takes Fasta file with peptide sequences. |
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108 * **--nr** Number of mutations. |
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109 * **--probability** Probability of mutating a sequence. |
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110 |
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111 2 **Filter Duplicates*** |
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112 * **--InFile** takes Fasta file with peptide sequences. |
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113 |
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114 3 **Keep Naturalaa** |
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115 * **--InFile** takes Fasta file with peptide sequences. |
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116 |
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117 4 **Filter Amino Acid** |
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118 * **--InFile** takes Fasta file with peptide sequences. |
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119 |
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120 ----- |
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121 |
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122 **Outputs** |
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123 * Returns a fasta file.]]></help> |
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124 |
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125 <citations> |
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126 <citation type="bibtex"> |
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127 @misc{PDAUGGITHUB, |
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128 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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129 year = {2020}, |
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130 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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131 publisher = {GitHub}, |
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132 journal = {GitHub repository}, |
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133 url = |
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134 {https://github.com/jaidevjoshi83/pdaug.git}, |
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135 } |
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136 </citation> |
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137 |
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138 <citation type="bibtex"> |
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139 @article{müller_gabernet_hiss_schneider_2017, |
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140 title={modlAMP: Python for antimicrobial peptides}, |
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141 volume={33}, |
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142 DOI={10.1093/bioinformatics/btx285}, |
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143 number={17}, |
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144 journal={Bioinformatics}, |
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145 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, |
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146 year={2017}, |
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147 pages={2753–2755} |
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148 } |
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149 </citation> |
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150 </citations> |
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151 </tool> |
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152 |
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153 |
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154 |