Mercurial > repos > jay > pdaug_peptide_data_access

annotate PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml @ 5:20a0454c5347 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author jay
date Thu, 28 Jan 2021 03:54:21 +0000
parents f85327600c11
children 24184ea66557
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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 $SelectDatasets.DataBaseType == "query_apd"
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17 -L '$SelectDatasets.list1'
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18 #end if
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20 #if $SelectDatasets.DataBaseType == "query_camp"
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21 -L '$SelectDatasets.list2'
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22 #end if
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24 ]]></command>
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27 <inputs>
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29 <conditional name="SelectDatasets">
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31 <param name="DataBaseType" type="select" label="Datasets" argument="--DataBaseType" help="Name of the data set.">
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32 <option value="AMPvsTMP" selected="true" > AMPvsTMP </option>
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33 <option value="AMPvsUniProt" > AMPvsUniProt </option>
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34 <option value="ACPvsTMP"> ACPvsTMP </option>
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35 <option value="ACPvsRandom"> ACPvsRandom </option>
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36 <option value="query_apd"> Query APD Database</option>
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37 <option value="query_camp" > Query CAMP Database </option>
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38 </param>
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42 <when value="AMPvsTMP"/>
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43 <when value="AMPvsUniProt"/>
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44 <when value="ACPvsTMP"/>
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45 <when value="ACPvsRandom"/>
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46 <when value="query_apd">
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47 <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
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48 </when>
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50 <when value="query_camp">
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51 <param name="list2" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
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52 </when>
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54 </conditional>
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57 </inputs>
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59 <outputs>
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60 <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" />
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61 </outputs>
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63 <tests>
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64 <test>
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65 <param name="DataBaseType" value="AMPvsTMP"/>
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66 <output name="output1" file="Out.tsv"/>
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67 </test>
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68
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69 <!-- 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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70 <test>
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71 <param name="DataBaseType" value="query_apd"/>
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72 <param name="list1" value="4,5,6" />
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73 <output name="output1" file="apd.tsv" lines_diff="8"/>
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74 </test>
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75 -->
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77 <test>
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78 <param name="DataBaseType" value="query_camp"/>
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79 <param name="list2" value="3,4,5,9" />
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80 <output name="output1" file="camp.tsv" lines_diff="10"/>
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81 </test>
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82
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83
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84 </tests>
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85
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86 <help><![CDATA[
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87 .. class:: infomark
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88
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89 **What it does**
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90
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91 This tool returns inbuild peptide data sets.
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92
1
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93 * **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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94 * **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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95 * **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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96 * **ACPvsRandom** ACP sequences from the CancerPPD database versus Random peptides generated randomly with the amino acid composition of AMPs.
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97 * **query_apd** Retrive sequences from the antimicrobial peptide database APD.
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98 * **query_camp** Retrive sequences from the antimicrobial peptide database CAMP.
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99
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100 -----
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101
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102 **Inputs**
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103 * **--DataBaseType** Takes dataset name as input.
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104
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105 -----
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106
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107 **Outputs**
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108 * Returns a tabular file with peptide sequences and class labels.]]></help>
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109
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110
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111 <citations>
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112 <citation type="bibtex">
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113 @misc{PDAUGGITHUB,
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114 author = {Joshi, Jayadev and Blankenberg, Daniel},
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115 year = {2020},
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116 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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117 publisher = {GitHub},
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118 journal = {GitHub repository},
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119 url =
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120 {https://github.com/jaidevjoshi83/pdaug.git},
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121 }
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122 </citation>
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123
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124 <citation type="bibtex">
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125 @article{müller_gabernet_hiss_schneider_2017,
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126 title={modlAMP: Python for antimicrobial peptides},
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127 volume={33},
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128 DOI={10.1093/bioinformatics/btx285},
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129 number={17},
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130 journal={Bioinformatics},
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131 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
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132 year={2017},
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133 pages={2753–2755}
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134 }
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135 </citation>
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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