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