Mercurial > repos > jay > pdaug_peptide_data_access

annotate PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml @ 0:6c12ca9f5d88 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 01:59:25 +0000
parents
children f85327600c11
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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="AMPvsTM" selected="true" > AMPvsTM </option>
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33 <option value="AMPvsUniProt" > AMPvsUniProt </option>
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34 <option value="ACPvsTM"> ACPvsTM </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="query_apd">
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43 <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" />
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44 </when>
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45
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46 <when value="query_camp">
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47 <param name="list2" 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 </conditional>
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53 </inputs>
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54
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55 <outputs>
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56 <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" />
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57 </outputs>
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58
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59 <tests>
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60 <test>
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61 <param name="DataBaseType" value="AMPvsTM"/>
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62 <output name="output1" file="out.tsv"/>
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63 </test>
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65 <test>
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66 <param name="DataBaseType" value="query_apd"/>
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67 <param name="list1" value="4,5,6" />
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68 <output name="output1" file="apd.tsv" lines_diff="8"/>
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69 </test>
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71 <test>
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72 <param name="DataBaseType" value="query_camp"/>
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73 <param name="list2" value="3,4,5,9" />
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74 <output name="output1" file="camp.tsv" lines_diff="10"/>
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75 </test>
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78 </tests>
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80 <help><![CDATA[
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81 .. class:: infomark
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83 **What it does**
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84
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85 This tool returns inbuild peptide data sets.
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86
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87 * **AMPvsTM** This option returns Antimicrobial peptides and transmembrane sequences.
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88 * **AMPvsUniProt** This option returns AMPs from the APD3 and other peptides from the UniProt database.
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89 * **ACPvsTM** This option returns anticancer peptides (CancerPPD) and helical transmembrane sequences.
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90 * **ACPvsRandom** This option returns anticancer peptides (CancerPPD) and random scrambled AMP sequences.
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91
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92 -----
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94 **Inputs**
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95 * **--DataBaseType** Takes dataset name as input.
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96
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97 -----
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98
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99 **Outputs**
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100 * Returns a tabular file with peptide sequences and class labels.]]></help>
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101
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102
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103 <citations>
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104 <citation type="bibtex">
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105 @misc{PDAUGGITHUB,
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106 author = {Joshi, Jayadev and Blankenberg, Daniel},
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107 year = {2020},
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108 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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109 publisher = {GitHub},
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110 journal = {GitHub repository},
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111 url =
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112 {https://github.com/jaidevjoshi83/pdaug.git},
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113 }
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114 </citation>
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115
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116 <citation type="bibtex">
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117 @article{müller_gabernet_hiss_schneider_2017,
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118 title={modlAMP: Python for antimicrobial peptides},
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119 volume={33},
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120 DOI={10.1093/bioinformatics/btx285},
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121 number={17},
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122 journal={Bioinformatics},
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123 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
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124 year={2017},
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125 pages={2753–2755}
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126 }
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127 </citation>
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128 </citations>
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129 </tool>
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130
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131
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132