Mercurial > repos > jay > pdaug_sequence_based_peptide_generation

annotate PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.xml @ 6:dd21da1ac55c draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author jay
date Sun, 31 Jan 2021 02:26:52 +0000
parents 93f7668caa55
children
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1 <tool id="pdaug_sequence_based_peptide_generation" name="PDAUG Sequence Based Peptide Generation" version="0.1.0">
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2 <description>Generates peptide sequence library</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 </requirements>
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7 <stdio>
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8 <exit_code range="1" level="fatal" />
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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13 python '$__tool_directory__/PDAUG_Sequence_Based_Peptide_Generation.py' '$SelMethod.Method'
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15 --outputFile '$output1'
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17 #if $SelMethod.Method == 'MutatedPeptides'
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18 --sequence '$SelMethod.input1'
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19 --mutation_site_list '$SelMethod.mutation_site_list'
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20 --AA_list '$SelMethod.AA_list'
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21 #end if
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23 #if $SelMethod.Method == 'RandomPeptides'
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24 --AA_list '$SelMethod.AA_list'
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25 --pep_length '$SelMethod.pep_length'
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26 --out_pep_lenght '$SelMethod.out_pep_length'
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27 #end if
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29 #if $SelMethod.Method == 'SlidingWindowPeptide'
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30 --InFile '$SelMethod.input1'
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31 --winSize '$SelMethod.WinSize'
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32 --FragSize '$SelMethod.FragSize'
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33 #end if
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35 ]]></command>
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37 <inputs>
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38 <conditional name='SelMethod' >
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40 <param name="Method" type="select" label="Methods to generate peptides " argument="">
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41 <option value="MutatedPeptides">Mutated Peptides</option>
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42 <option value="RandomPeptides">Random Peptides</option>
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43 <option value="SlidingWindowPeptide">Sliding Window Peptide</option>
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44 </param>
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46 <when value="MutatedPeptides">
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47 <param name="input1" type="text" label="Peptide sequence" value="KLLKLLKKKLLK" argument= "--sequence" help="Peptide sequence"/>
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48 <param name="mutation_site_list" label="Mutation Site" value="2" type="text" argument="--mutation_site_list" help="List of integer to introduce mutation"/>
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49 <param name="AA_list" type="text" label="Amino Acide List" value="I,H" argument="-AA_list" help="List of amino acids to be replaced"/>
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50 </when>
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51
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52 <when value="RandomPeptides">
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53 <param name="AA_list" type="text" label="Amino Acide List" value="G,L,F,D,I,V,K" argument="-AA_list" help="List of amino acids" />
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54 <param name="pep_length" type="integer" optional="false" label="Peptide Legnth" value="7" argument="--pep_length" help="Length of output peptide"/>
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55 <param name="out_pep_length" type="integer" optional="false" label="Nomber of peptides" value="7" argument="--out_pep_length" help="Number of peptides to be generated"/>
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56 </when>
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57
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58 <when value="SlidingWindowPeptide">
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59 <param name="input1" type="data" label="Input Sequence" format="fasta" argument= "--InFile" help="Input protein sequence"/>
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60 <param name="WinSize" type="integer" label="Window Size" value="3" argument="--winSize" help="Sliding window size" />
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61 <param name="FragSize" type="integer" label="Fragment Size" value="7" argument="--FragSize" help="Size of the peptides" />
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62 </when>
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63 </conditional>
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64 </inputs>
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65
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66 <outputs>
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67 <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelMethod.Method} (fasta)" />
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name='Method' value="MutatedPeptides" />
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72 <param name='input1' value="KLLKLLKKKLLK" />
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73 <param name='mutation_site_list' value="2" />
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74 <param name='AA_list' value="G,Y" />
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75 <output name="output1" file="out1.fasta" />
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76 </test>
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77
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78 <test>
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79 <param name='Method' value="RandomPeptides" />
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80 <param name='AA_list' value="G,L,F,D,I,V,K," />
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81 <param name='pep_length' value="7" />
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82 <param name='out_pep_length' value="7" />
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83 <output name="output1" file="out2.fasta" lines_diff='28'/>
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84 </test>
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85
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86 <test>
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87 <param name='Method' value="SlidingWindowPeptide" />
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88 <param name='input1' value="test1.fasta" />
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89 <param name='WinSize' value="3" />
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90 <param name='FragSize' value="7" />
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91 <output name="output1" file="out3.fasta" />
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92 </test>
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93 </tests>
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94 <help><![CDATA[
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95 .. class:: infomark
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96
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97 **What it does**
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98
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99 This tool generates peptide sequences based on three sequences based properties which includes Mutated Peptides, Random Peptides, and Sliding Window Peptide.
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100
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101 -----
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102
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103 **Inputs**
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104 **1** MutatedPeptides
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105 * **--sequence** Input peptide sequence
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106 * **--mutation_site_list** Sites to mutated AA as Integer values
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107 * **--AA_list** List of amino acids to replace
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108
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109 **2** RandomPeptides
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110 * **--AA_list** List of amino acids
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111 * **--pep_length** Length of peptide sequences
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112 * **--out_pep_lenght** Number of output peptides
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113
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114 **3** SlidingWindowPeptide
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115 * **--InFile** Input protein sequences fasta file
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116 * **--winSize** Sliding window size
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117 * **--FragSize** Output Peptide sequence size
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118
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119 -----
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120
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121 **Outputs**
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122 * **--outputFile** Returns fasta files with peptide sequences. ]]></help>
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123 <citations>
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124 <citation type="bibtex">
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125 @misc{PDAUGGITHUB,
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126 author = {Joshi, Jayadev and Blankenberg, Daniel},
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127 year = {2020},
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128 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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129 publisher = {GitHub},
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130 journal = {GitHub repository},
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131 url =
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132 {https://github.com/jaidevjoshi83/pdaug.git},
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133 }
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134 </citation>
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135
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136 </citations>
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137 </tool>
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138
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139
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140