Mercurial > repos > jay > pdaug_peptide_core_functions

annotate PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml @ 9:4add768cb3d2 draft default tip

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author jay
date Wed, 12 Jan 2022 20:03:53 +0000
parents 851602577d38
children
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1 <tool id="pdaug_peptide_core_functions" name="PDAUG Peptide Core Functions" version="0.1.0">
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2 <description> Peptide sequence related core functions </description>
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4 <requirements>
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5 <requirement type="package" version="0.24.2">pandas</requirement>
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6 <requirement type="package" version="4.1.2">modlamp</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1" level="fatal" />
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10 </stdio>
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11 <command detect_errors="exit_code"><![CDATA[
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14 python '$__tool_directory__/PDAUG_Peptide_Core_Functions.py' '$SelCoreFunction.CoreFunction'
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16 --InFile '$InFile'
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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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21 #end if
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23 #if $SelCoreFunction.CoreFunction == 'filteraa'
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24 --FilterAA 'filterAA'
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25 #end if
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27 #if $SelCoreFunction.CoreFunction == 'filterduplicates'
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28 --FilterAA 'filterduplicates'
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29 #end if
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31 #if $SelCoreFunction.CoreFunction == 'keepnaturalaa'
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32 --FilterAA 'keepnaturalaa'
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33 #end if
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35 --FastOut '$output1'
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37 ]]></command>
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39 <inputs>
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41 <param name="InFile" type="data" format="fasta" label="Input file" argument= "--InFile" help="Input fasta file with peptides"/>
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43 <conditional name='SelCoreFunction' >
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45 <param name="CoreFunction" type="select" label="Analysis options" argument="">
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46 <option value="mutateAA">Mutate Amino Acid</option>
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47 <option value="filterduplicates">Filter Duplicates Peptides</option>
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48 <option value="keepnaturalaa">Remove Peptides With Unatural Amino Acids</option>
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49 <option value="filteraa">Filter Peptides With Specific Amino Acid</option>
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50 </param>
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52 <when value="mutateAA">
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53 <param name="nr" type="integer" label="Number of mutations" value="3" argument="--nr" help="Number of mutations"/>
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54 <param name="prob" type="float" label="Probability" value="1.0" argument="--Prob" help="Probability of mutating a sequence" />
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55 </when>
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57 <when value="filterduplicates">
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58 </when>
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59
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60 <when value="keepnaturalaa">
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61 </when>
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63 <when value="filteraa">
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64 <param name="FilterAA" type="text" value="eisenberg" label="Filter AA" argument="--FilterAA" help="Amino acids to be filtered" />
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65 </when>
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67 </conditional>
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68 </inputs>
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70 <outputs>
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71 <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelCoreFunction.CoreFunction} (fasta)" />
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="InFile" value="test1.fasta"/>
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76 <param name="CoreFunction" value="mutateAA" />
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77 <param name="nr" value="3"/>
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78 <param name="prob" value="1.0"/>
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79 <output name="output1" file="out1.fasta" lines_diff="2"/>
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80 </test>
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81 <test>
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82 <param name="InFile" value="test2.fasta"/>
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83 <param name="CoreFunction" value="filterduplicates" />
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84 <output name="output1" file="out2.fasta" />
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85 </test>
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86 <test>
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87 <param name="InFile" value="test3.fasta"/>
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88 <param name="CoreFunction" value="keepnaturalaa" />
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89 <output name="output1" file="out3.fasta" />
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90 </test>
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91 <test>
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92 <param name="InFile" value="test4.fasta"/>
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93 <param name="CoreFunction" value="filteraa" />
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94 <param name="FilterAA" value="eisenberg" />
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95 <output name="output1" file="out4.fasta" />
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99 .. class:: infomark
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100
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101 **What it does**
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102
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103 This tool performs some core functions on the peptide sequences and equipped with various options
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104
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105 * **Mutate Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly.
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106 * **Filter Duplicates Peptides** Method to filter duplicates in the sequences from the class attribute sequences.
0
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107 * **Keep Naturalaa** Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character.
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108 * **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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109
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110 -----
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111
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112 **Inputs**
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113
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114 1 **Mutate Amino Acid**
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115 * **--InFile** takes Fasta file with peptide sequences.
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116 * **--nr** Number of mutations.
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117 * **--probability** Probability of mutating a sequence.
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118
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119 2 **Filter Duplicates Peptides***
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120 * **--InFile** takes Fasta file with peptide sequences.
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121
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122 3 **Remove Peptides With Unatural Amino Acids**
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123 * **--InFile** takes Fasta file with peptide sequences.
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124
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125 4 **Filter Peptides With Specific Amino Acid**
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126 * **--InFile** takes Fasta file with peptide sequences.
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127
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128 -----
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129
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130 **Outputs**
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131 * Returns a fasta file.]]></help>
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132
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133 <citations>
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134 <citation type="bibtex">
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135 @misc{PDAUGGITHUB,
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136 author = {Joshi, Jayadev and Blankenberg, Daniel},
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137 year = {2020},
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138 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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139 publisher = {GitHub},
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140 journal = {GitHub repository},
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141 url =
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142 {https://github.com/jaidevjoshi83/pdaug.git},
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143 }
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144 </citation>
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145
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146 <citation type="bibtex">
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147 @article{müller_gabernet_hiss_schneider_2017,
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148 title={modlAMP: Python for antimicrobial peptides},
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149 volume={33},
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150 DOI={10.1093/bioinformatics/btx285},
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151 number={17},
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152 journal={Bioinformatics},
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153 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
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154 year={2017},
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155 pages={2753–2755}
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156 }
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157 </citation>
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158 </citations>
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159 </tool>