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annotate dbkit_create.xml @ 0:1914107cc967 draft

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"planemo upload commit 3632646bec5edbe47e06c894e32bfd215b895555-dirty"
author guerler
date Wed, 25 Nov 2020 17:22:48 +0000
parents
children 987e55ea29b8
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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 generator</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 mkdir temp &&
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5 python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$url' -t 'temp' -o '$index' -d '$database' -g '$log' -il '$advanced.idlength' -ic '$advanced.idcase' -ie '$advanced.idextension'
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6 ]]></command>
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7 <inputs>
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8 <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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9 <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source.">
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10 <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option>
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11 </param>
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12 <conditional name="advanced">
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13 <param name="type" type="boolean" label="Identifier Formatting Options" />
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14 <when value="true">
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15 <param name="idextension" type="text" label="Identifier Extensions" help="Specify the extension of the identifier (optional)."/>
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16 <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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17 <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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18 <option value="">Unformatted</option>
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19 <option value="lower">Lower</option>
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20 <option value="upper">Upper</option>
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21 </param>
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22 </when>
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23 <when value="false">
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24 <param name="idextension" type="hidden" value="" />
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25 <param name="idlength" type="hidden" value="0" />
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26 <param name="idcase" type="hidden" value="" />
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27 </when>
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data format="ffindex" name="index" label="DBKit Index"/>
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32 <data format="ffdata" name="database" label="DBKit Database" />
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33 <data format="txt" name="log" label="DBKit Log" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" value="create/chains.tabular" />
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38 <param name="url" value="https://files.rcsb.org/download/" />
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39 <conditional name="advanced">
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40 <param name="type" value="true" />
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41 <param name="idextension" value="pdb" />
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42 <param name="idlength" value="4" />
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43 <param name="idcase" value="lower" />
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44 </conditional>
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45 <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
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46 <output name="index" file="create/index.ffindex" />
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47 <output name="database" file="create/data.ffdata" />
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 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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52 generated indicating the start and end of every entry within the database file.
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53 ]]></help>
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54 </tool>