Mercurial > repos > guerler > ffindex_dbkit_create

annotate dbkit_create.xml @ 2:d97c5316e813 draft

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"planemo upload commit 2a0fc8275bfbb76a828082424d346bbe0fd40914"
author guerler
date Thu, 01 Apr 2021 19:36:49 +0000
parents c1dff5c2a7b3
children
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1 <tool id="ffindex_dbkit_create" name="DBKit Create" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01">
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2 <description>database</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir -p inputs &&
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9 #for item in $inputs
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10 ln -s '${item}' 'inputs/${item.element_identifier}' &&
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11 #end for
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12 dbkit_create.py
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13 -l '$input'
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14 -p 'inputs'
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15 -o '$index'
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16 -d '$database'
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17 -g '$log'
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18 -il '$advanced.idlength'
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19 -ic '$advanced.idcase'
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20 -ie '$advanced.idextension'
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21 -ip '$advanced.idprefix'
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22 ]]> </command>
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23 <inputs>
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24 <param name="input" type="data" format="tabular" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded." />
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25 <param name="inputs" type="data" format="txt" multiple="true" label="Specify your datasets" help="The datasets that you want to convert into an ffindex." />
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26 <conditional name="advanced">
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27 <param name="type" type="select" label="Identifier Formatting Options" help="">
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28 <option value="true">Yes, I want to format my identifiers</option>
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29 <option value="false">No formatting</option>
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30 </param>
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31 <when value="true">
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32 <param name="idprefix" type="text" optional="true" label="Identifier Prefix" help="Specify the prefix of the identifier">
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33 <validator type="regex" message="Please only use letters, numbers or underscores">^[a-zA-Z.]+$</validator>
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34 </param>
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35 <param name="idextension" type="text" optional="true" label="Identifier Extensions" help="Specify the extension of the identifier">
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36 <validator type="regex" message="Please only use letters, numbers or underscores">^[a-zA-Z.]+$</validator>
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37 </param>
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38 <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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39 <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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40 <option value="">Unformatted</option>
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41 <option value="lower">Lower</option>
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42 <option value="upper">Upper</option>
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43 </param>
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44 </when>
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45 <when value="false">
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46 <param name="idprefix" type="hidden" value="" />
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47 <param name="idextension" type="hidden" value="" />
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48 <param name="idlength" type="hidden" value="0" />
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49 <param name="idcase" type="hidden" value="" />
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50 </when>
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51 </conditional>
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52 <expand macro="logfile" />
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53 </inputs>
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54 <outputs>
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55 <data name="index" format="ffindex" label="DBKit Index" />
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56 <data name="database" format="ffdata" label="DBKit Database" />
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57 <data format="txt" name="log" label="DBKit Log">
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58 <filter>logfile</filter>
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59 </data>
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60 </outputs>
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61 <tests>
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62 <test expect_num_outputs="2">
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63 <param name="input" value="create/sequences.tabular" ftype="tabular" />
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64 <param name="inputs" value="create/NP_000282.1.hhr,create/NP_000290.2.hhr,create/NP_000548.2.hhr,create/NP_000836.2.hhr" />
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65 <conditional name="advanced">
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66 <param name="type" value="false" />
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67 </conditional>
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68 <output name="index" file="create/sequences.ffindex" ftype="ffindex" />
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69 <output name="database" file="create/sequences.ffdata" ftype="ffdata" />
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73
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74 **What it does**
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75
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76 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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77 generated indicating the start and size of every entry within the database file. The tool can also operate on collections.
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78 ]]> </help>
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79 <expand macro="citations" />
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80 </tool>