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annotate dbkit_create.xml @ 3:03e124ff7e26 draft

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"planemo upload commit bd03b7888eab0b010acfc3affd38bf4d4e2bb1ef-dirty"
author guerler
date Wed, 16 Dec 2020 13:11:35 +0000
parents 81c7d4668a7e
children
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1 <tool id="dbkit_create" name="DBKit Create" version="0.1.1" python_template_version="3.5" license="MIT">
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2 <description>database</description>
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3 <requirements>
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4 <requirement type="package" version="3.2">python-wget</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #if str($source.type) == "false":
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8 mkdir -p inputs &&
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9 #for item in $source.inputs
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10 cp '${str(item)}' 'inputs/${item.element_identifier}' &&
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11 #end for
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12 #end if
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13 python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$source.url' -p 'inputs' -o '$index' -d '$database' -g '$log' -il '$advanced.idlength' -ic '$advanced.idcase' -ie '$advanced.idextension'
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14 ]]></command>
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15 <inputs>
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16 <param format="tabular" name="input" type="data" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded."/>
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17 <conditional name="source">
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18 <param name="type" type="boolean" label="Download from URL"/>
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19 <when value="true">
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20 <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source.">
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21 <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option>
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22 </param>
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23 <param name="inputs" type="hidden"/>
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24 </when>
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25 <when value="false">
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26 <param name="url" type="hidden"/>
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27 <param name="inputs" type="data_collection" collection_type="list" label="Collection" help="Specify a collection containing the datasets."/>
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28 </when>
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29 </conditional>
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30 <conditional name="advanced">
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31 <param name="type" type="boolean" label="Identifier Formatting Options" />
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32 <when value="true">
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33 <param name="idextension" type="text" label="Identifier Extensions" help="Specify the extension of the identifier (optional)."/>
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34 <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)."/>
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35 <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional).">
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36 <option value="">Unformatted</option>
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37 <option value="lower">Lower</option>
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38 <option value="upper">Upper</option>
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39 </param>
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40 </when>
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41 <when value="false">
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42 <param name="idextension" type="hidden" value="" />
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43 <param name="idlength" type="hidden" value="0" />
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44 <param name="idcase" type="hidden" value="" />
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45 </when>
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46 </conditional>
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47 </inputs>
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48 <outputs>
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49 <data format="ffindex" name="index" label="DBKit Index"/>
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50 <data format="ffdata" name="database" label="DBKit Database" />
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51 <data format="txt" name="log" label="DBKit Log" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input" value="create/chains.tabular" />
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56 <conditional name="source">
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57 <param name="type" value="true"/>
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58 <param name="url" value="https://files.rcsb.org/download/" />
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59 </conditional>
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60 <conditional name="advanced">
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61 <param name="type" value="true" />
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62 <param name="idextension" value="pdb" />
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63 <param name="idlength" value="4" />
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64 <param name="idcase" value="lower" />
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65 </conditional>
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66 <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
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67 <output name="index" file="create/first.ffindex" />
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68 <output name="database" file="create/first.ffdata" />
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69 </test>
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70 <test>
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71 <param name="input" value="create/sequences.tabular" />
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72 <conditional name="source">
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73 <param name="type" value="false"/>
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74 <param name="inputs">
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75 <collection type="list">
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76 <element name="NP_000282.1.hhr" value="create/NP_000282.1.hhr" />
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77 <element name="NP_000290.2.hhr" value="create/NP_000290.2.hhr" />
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78 <element name="NP_000548.2.hhr" value="create/NP_000548.2.hhr" />
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79 <element name="NP_000836.2.hhr" value="create/NP_000836.2.hhr" />
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80 </collection>
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81 </param>
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82 </conditional>
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83 <conditional name="advanced">
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84 <param name="type" value="false" />
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85 </conditional>
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86 <output name="index" file="create/sequences.ffindex" />
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87 <output name="database" file="create/sequences.ffdata" />
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is
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92 generated indicating the start and size of every entry within the database file. The tool can also operate on collections.
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93 ]]></help>
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94 </tool>