Mercurial > repos > jay > pdaug_peptide_data_access

annotate PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml @ 7:24184ea66557 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author jay
date Sun, 09 Jan 2022 03:52:11 +0000
parents 20a0454c5347
children
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1 <tool id="pdaug_peptide_data_access" name="PDAUG Peptide Data Access" version="0.1.0">
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2 <description>Fetch peptide data from inbuild datasets and public databases</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 <requirement type="package" version="8.0.21">mysql-connector-python</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1" level="fatal" />
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11 </stdio>
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12 <command detect_errors="exit_code"><![CDATA[
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14 python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1'
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16 #if $SelectDatasets.DataBaseType == "AMPvsTMP"
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17 -d 'AMPvsTMP'
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18 #end if
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20 #if $SelectDatasets.DataBaseType == "AMPvsUniProt"
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21 -d 'AMPvsUniProt'
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22 #end if
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24 #if $SelectDatasets.DataBaseType == "ACPvsTMP"
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25 -d 'ACPvsTMP'
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26 #end if
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28 #if $SelectDatasets.DataBaseType == "ACPvsRandom"
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29 -d 'ACPvsRandom'
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30 #end if
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32 #if $SelectDatasets.DataBaseType == "query_apd"
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33 -L '$SelectDatasets.list1'
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34 #end if
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36 #if $SelectDatasets.DataBaseType == "query_camp"
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37 -L '$SelectDatasets.list1'
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38 #end if
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40 ]]></command>
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43 <inputs>
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45 <conditional name="SelectDatasets">
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47 <param name="DataBaseType" type="select" label="Datasets" argument="--DataBaseType" help="Name of the data set.">
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48 <option value="AMPvsTMP" selected="true" > AMPvsTMP </option>
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49 <option value="AMPvsUniProt" > AMPvsUniProt </option>
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50 <option value="ACPvsTMP"> ACPvsTMP </option>
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51 <option value="ACPvsRandom"> ACPvsRandom </option>
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52 <option value="query_apd"> Query APD Database</option>
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53 <option value="query_camp" > Query CAMP Database </option>
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54 </param>
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55
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56 <when value="AMPvsTMP">
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57
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58 </when>
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59
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60 <when value="AMPvsUniProt">
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62 </when>
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64 <when value="ACPvsTMP">
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65 </when>
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67 <when value="ACPvsRandom">
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68 </when>
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69
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70 <when value="query_apd">
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71 <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
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72 </when>
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73
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74 <when value="query_camp">
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75 <param name="list2" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
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76 </when>
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78 </conditional>
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81 </inputs>
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83 <outputs>
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84 <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" />
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85 </outputs>
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87 <tests>
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88 <test>
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89 <param name="DataBaseType" value="AMPvsTMP"/>
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90 <output name="output1" file="Out.tsv"/>
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91 </test>
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92
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93 <!-- This test has consistently failed over several months, due to inability to access host/URL http://aps.unmc.edu/AP/database/query_output.php?ID=00004
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94 <test>
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95 <param name="DataBaseType" value="query_apd"/>
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96 <param name="list1" value="4,5,6" />
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97 <output name="output1" file="apd.tsv" lines_diff="8"/>
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98 </test>
5
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99 -->
0
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100
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101 <test>
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102 <param name="DataBaseType" value="query_camp"/>
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103 <param name="list2" value="3,4,5,9" />
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104 <output name="output1" file="camp.tsv" lines_diff="10"/>
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105 </test>
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106
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107
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108 </tests>
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109
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110 <help><![CDATA[
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111 .. class:: infomark
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112
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113 **What it does**
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114
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115 This tool returns inbuild peptide data sets.
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116
1
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117 * **AMPvsTMP** Antimicrobial peptides (AMP) consist of an intersection of all activity annotations of the APD2 and CAMP databases, where gram-positive, gram-negative, and antifungal exact matches were observed versus transmenbrane peptides (TMP) extracted from alpha-helical transmembrane regions of proteins for classification.
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118 * **AMPvsUniProt** AMP consisting of the whole APD3 versus UniProt peptides randomly extracted from the UniProt database, to be used for classification.
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119 * **ACPvsTMP** Anticancer Peptide (ACP) sequences from the CancerPPD database versus TM extracted from alpha-helical transmembrane regions of proteins for classification.
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120 * **ACPvsRandom** ACP sequences from the CancerPPD database versus Random peptides generated randomly with the amino acid composition of AMPs.
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121 * **query_apd** Retrive sequences from the antimicrobial peptide database APD.
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122 * **query_camp** Retrive sequences from the antimicrobial peptide database CAMP.
0
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123
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124 -----
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125
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126 **Inputs**
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127 * **--DataBaseType** Takes dataset name as input.
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128
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129 -----
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130
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131 **Outputs**
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132 * Returns a tabular file with peptide sequences and class labels.]]></help>
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133
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134
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135 <citations>
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136 <citation type="bibtex">
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137 @misc{PDAUGGITHUB,
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138 author = {Joshi, Jayadev and Blankenberg, Daniel},
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139 year = {2020},
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140 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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141 publisher = {GitHub},
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142 journal = {GitHub repository},
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143 url =
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144 {https://github.com/jaidevjoshi83/pdaug.git},
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145 }
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146 </citation>
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147
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148 <citation type="bibtex">
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149 @article{müller_gabernet_hiss_schneider_2017,
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150 title={modlAMP: Python for antimicrobial peptides},
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151 volume={33},
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152 DOI={10.1093/bioinformatics/btx285},
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153 number={17},
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154 journal={Bioinformatics},
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155 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
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156 year={2017},
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157 pages={2753–2755}
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158 }
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159 </citation>
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160 </citations>
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161 </tool>
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162
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163
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164