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comparison dbkit_create.xml @ 2:81c7d4668a7e draft

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"planemo upload commit bd03b7888eab0b010acfc3affd38bf4d4e2bb1ef-dirty"
author guerler
date Wed, 16 Dec 2020 12:02:48 +0000
parents 987e55ea29b8
children 03e124ff7e26
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1:987e55ea29b8 2:81c7d4668a7e
1 <tool id="dbkit_create" name="DBKit Create" version="0.1.1" python_template_version="3.5" license="MIT"> 1 <tool id="dbkit_create" name="DBKit Create" version="0.1.1" python_template_version="3.5" license="MIT">
2 <description>database generator</description> 2 <description>database generator</description>
3 <command detect_errors="exit_code"><![CDATA[ 3 <command detect_errors="exit_code"><![CDATA[
4 mkdir temp && 4 #if str($source.type) == "false":
5 python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$url' -o '$index' -d '$database' -g '$log' -il '$advanced.idlength' -ic '$advanced.idcase' -ie '$advanced.idextension' 5 mkdir -p inputs &&
6 #for item in $source.inputs
7 cp '${str(item)}' 'inputs/${item.element_identifier}' &&
8 #end for
9 #end if
10 python3 '$__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'
6 ]]></command> 11 ]]></command>
7 <inputs> 12 <inputs>
8 <param format="tabular" name="input" type="data" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded."/> 13 <param format="tabular" name="input" type="data" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded."/>
9 <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source."> 14 <conditional name="source">
10 <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option> 15 <param name="type" type="boolean" label="Download from URL"/>
11 </param> 16 <when value="true">
17 <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source.">
18 <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option>
19 </param>
20 <param name="inputs" type="hidden"/>
21 </when>
22 <when value="false">
23 <param name="url" type="hidden"/>
24 <param name="inputs" type="data_collection" collection_type="list" label="Collection" help="Specify a collection containing the datasets."/>
25 </when>
26 </conditional>
12 <conditional name="advanced"> 27 <conditional name="advanced">
13 <param name="type" type="boolean" label="Identifier Formatting Options" /> 28 <param name="type" type="boolean" label="Identifier Formatting Options" />
14 <when value="true"> 29 <when value="true">
15 <param name="idextension" type="text" label="Identifier Extensions" help="Specify the extension of the identifier (optional)."/> 30 <param name="idextension" type="text" label="Identifier Extensions" help="Specify the extension of the identifier (optional)."/>
16 <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)."/> 31 <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)."/>
33 <data format="txt" name="log" label="DBKit Log" /> 48 <data format="txt" name="log" label="DBKit Log" />
34 </outputs> 49 </outputs>
35 <tests> 50 <tests>
36 <test> 51 <test>
37 <param name="input" value="create/chains.tabular" /> 52 <param name="input" value="create/chains.tabular" />
38 <param name="url" value="https://files.rcsb.org/download/" /> 53 <conditional name="source">
54 <param name="type" value="true"/>
55 <param name="url" value="https://files.rcsb.org/download/" />
56 </conditional>
39 <conditional name="advanced"> 57 <conditional name="advanced">
40 <param name="type" value="true" /> 58 <param name="type" value="true" />
41 <param name="idextension" value="pdb" /> 59 <param name="idextension" value="pdb" />
42 <param name="idlength" value="4" /> 60 <param name="idlength" value="4" />
43 <param name="idcase" value="lower" /> 61 <param name="idcase" value="lower" />
44 </conditional> 62 </conditional>
45 <param format="tabular" name="database" value="roc/biogrid_fret.txt" /> 63 <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
46 <output name="index" file="create/index.ffindex" /> 64 <output name="index" file="create/first.ffindex" />
47 <output name="database" file="create/data.ffdata" /> 65 <output name="database" file="create/first.ffdata" />
66 </test>
67 <test>
68 <param name="input" value="create/sequences.tabular" />
69 <conditional name="source">
70 <param name="type" value="false"/>
71 <param name="inputs">
72 <collection type="list">
73 <element name="NP_000282.1.hhr" value="create/NP_000282.1.hhr" />
74 <element name="NP_000290.2.hhr" value="create/NP_000290.2.hhr" />
75 <element name="NP_000548.2.hhr" value="create/NP_000548.2.hhr" />
76 <element name="NP_000836.2.hhr" value="create/NP_000836.2.hhr" />
77 </collection>
78 </param>
79 </conditional>
80 <conditional name="advanced">
81 <param name="type" value="false" />
82 </conditional>
83 <output name="index" file="create/sequences.ffindex" />
84 <output name="database" file="create/sequences.ffdata" />
48 </test> 85 </test>
49 </tests> 86 </tests>
50 <help><![CDATA[ 87 <help><![CDATA[
51 This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is 88 This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is
52 generated indicating the start and end of every entry within the database file. 89 generated indicating the start and size of every entry within the database file. The tool can also operate on collections.
53 ]]></help> 90 ]]></help>
54 </tool> 91 </tool>