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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/extract_element_from_collection commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
author erasmus-medical-center
date Wed, 13 Dec 2017 10:09:11 -0500
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c46360dcbf3f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/extract_element_from_collection commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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1 <tool id="extract_element_from_collection" name="Extract Element" version="0.1" profile="16.07">
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2 <description>from a collection based on name</description>
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3 <command detect_errors="aggressive"><![CDATA[
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4 echo 'no element with name $elementname found in your collection' > '$output'
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5
c46360dcbf3f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/extract_element_from_collection commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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6 && mkdir elementoutputs
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7 #for $dataset in $input_collection:
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8 && echo $dataset.element_identifier
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9 #if $elementname == ''
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10 && cp $dataset 'elementoutputs/$dataset.element_identifier'
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11 #elif $dataset.element_identifier == $elementname:
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12 && cp $dataset '$output'
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13 #end if
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14 #end for
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15 ]]></command>
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16 <inputs>
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17 <param name="input_collection" type="data_collection" collection_type="list" label="Input Collection"/>
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18 <!-- find a way to make a select from all elements? -->
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19 <param name="elementname" type="text" value="" label="name of collection element to extract" help="if left blank, all files will be extracted"/>
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="auto" label="${elementname}">
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23 <filter>elementname != ''</filter>
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24 </data>
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25 <data format="auto" name="extracted">
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26 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="elementoutputs" visible="true" assign_primary_output="true"/>
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27 <filter>elementname == ''</filter>
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28 </data>
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29 </outputs>
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30 <tests>
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31 <test><!-- test with valid element -->
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32 <param name="input_collection">
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33 <collection type="list">
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34 <element name="element1" value="example.mothur.shared" />
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35 <element name="element2" value="multisample.taxonomy" />
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36 </collection>
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37 </param>
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38 <param name="elementname" value="element2"/>
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39 <output name="output" file="multisample.taxonomy"/>
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40 </test>
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41 <test><!-- test with invalid element -->
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42 <param name="input_collection">
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43 <collection type="list">
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44 <element name="element1" value="example.mothur.shared" />
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45 <element name="element2" value="multisample.taxonomy" />
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46 </collection>
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47 </param>
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48 <param name="elementname" value="element3"/>
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49 <output name="output">
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50 <assert_contents>
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51 <has_text text="no element with name"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57 **What it does**
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58 extract a dataset from a collection based on name
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59 ]]></help>
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60 <citations>
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61 </citations>
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62 </tool>