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comparison PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml @ 1:f85327600c11 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
author jay
date Tue, 29 Dec 2020 04:11:02 +0000
parents 6c12ca9f5d88
children 20a0454c5347
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0:6c12ca9f5d88 1:f85327600c11
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 13
14 python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1' 14 python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1'
15 15
16 #if $SelectDatasets.DataBaseType == "query_apd" 16 #if $SelectDatasets.DataBaseType == "query_apd"
17 -L $SelectDatasets.list1 17 -L '$SelectDatasets.list1'
18 #end if 18 #end if
19 19
20 #if $SelectDatasets.DataBaseType == "query_camp" 20 #if $SelectDatasets.DataBaseType == "query_camp"
21 -L $SelectDatasets.list2 21 -L '$SelectDatasets.list2'
22 #end if 22 #end if
23 23
24 ]]></command> 24 ]]></command>
25 25
26 26
27 <inputs> 27 <inputs>
28 28
29 <conditional name="SelectDatasets"> 29 <conditional name="SelectDatasets">
30 30
31 <param name="DataBaseType" type="select" label="Datasets" argument="--DataBaseType" help="Name of the data set."> 31 <param name="DataBaseType" type="select" label="Datasets" argument="--DataBaseType" help="Name of the data set.">
32 <option value="AMPvsTM" selected="true" > AMPvsTM </option> 32 <option value="AMPvsTMP" selected="true" > AMPvsTMP </option>
33 <option value="AMPvsUniProt" > AMPvsUniProt </option> 33 <option value="AMPvsUniProt" > AMPvsUniProt </option>
34 <option value="ACPvsTM"> ACPvsTM </option> 34 <option value="ACPvsTMP"> ACPvsTMP </option>
35 <option value="ACPvsRandom"> ACPvsRandom </option> 35 <option value="ACPvsRandom"> ACPvsRandom </option>
36 <option value="query_apd"> Query APD Database</option> 36 <option value="query_apd"> Query APD Database</option>
37 <option value="query_camp" > Query CAMP Database </option> 37 <option value="query_camp" > Query CAMP Database </option>
38 </param> 38 </param>
39 39
56 <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" /> 56 <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" />
57 </outputs> 57 </outputs>
58 58
59 <tests> 59 <tests>
60 <test> 60 <test>
61 <param name="DataBaseType" value="AMPvsTM"/> 61 <param name="DataBaseType" value="AMPvsTMP"/>
62 <output name="output1" file="out.tsv"/> 62 <output name="output1" file="Out.tsv"/>
63 </test> 63 </test>
64 64
65 <test> 65 <test>
66 <param name="DataBaseType" value="query_apd"/> 66 <param name="DataBaseType" value="query_apd"/>
67 <param name="list1" value="4,5,6" /> 67 <param name="list1" value="4,5,6" />
82 82
83 **What it does** 83 **What it does**
84 84
85 This tool returns inbuild peptide data sets. 85 This tool returns inbuild peptide data sets.
86 86
87 * **AMPvsTM** This option returns Antimicrobial peptides and transmembrane sequences. 87 * **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.
88 * **AMPvsUniProt** This option returns AMPs from the APD3 and other peptides from the UniProt database. 88 * **AMPvsUniProt** AMP consisting of the whole APD3 versus UniProt peptides randomly extracted from the UniProt database, to be used for classification.
89 * **ACPvsTM** This option returns anticancer peptides (CancerPPD) and helical transmembrane sequences. 89 * **ACPvsTMP** Anticancer Peptide (ACP) sequences from the CancerPPD database versus TM extracted from alpha-helical transmembrane regions of proteins for classification.
90 * **ACPvsRandom** This option returns anticancer peptides (CancerPPD) and random scrambled AMP sequences. 90 * **ACPvsRandom** ACP sequences from the CancerPPD database versus Random peptides generated randomly with the amino acid composition of AMPs.
91 * **query_apd** Retrive sequences from the antimicrobial peptide database APD.
92 * **query_camp** Retrive sequences from the antimicrobial peptide database CAMP.
91 93
92 ----- 94 -----
93 95
94 **Inputs** 96 **Inputs**
95 * **--DataBaseType** Takes dataset name as input. 97 * **--DataBaseType** Takes dataset name as input.