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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
author ecology
date Sun, 06 Mar 2022 22:10:01 +0000
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217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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1 <tool id="xmlstarlet" name="xmlstarlet" version="1.6.1">
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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2 <description>convert a metadata XML file in one standard to another</description>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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3 <requirements>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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4 <requirement type="package" version="1.6.1">xmlstarlet</requirement>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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5 </requirements>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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6 <command detect_errors="exit_code"><![CDATA[
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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7 xml tr '$xsl' '$input' > '$output'
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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8 ]]>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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9 </command>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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10 <inputs>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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11 <param name="input" type="data" format="xml" label="input xml file to convert" help="A xml file corresponding to a xsd schema you want to convert in another." />
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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12 <param name="xsl" type="data" format="xml" label="input xsl convertion file" help="A xsl file describing the mapping between a first xsd specification to another." />
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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13 </inputs>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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14 <outputs>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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15 <data name="output" format="xml" label="${tool.name} on ${on_string}: Converted xml" />
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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16 </outputs>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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17 <tests>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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18 <!-- Ensure conversion works -->
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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19 <test expect_num_outputs="1">
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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20 <param name="input" value="input_standardiso19115.xml" ftype="xml"/>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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21 <param name="xsl" value="iso2eml_all_in_one.xsl" ftype="xml"/>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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22 <output name="output" file="output_standardEML.xml" />
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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23 </test>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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24 </tests>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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25 <help>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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26
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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27 .. class:: infomark
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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28
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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29 **What it does**
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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30
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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31 This tool converts a xml file to another using a xsl coversion file to specify the translation to be done, from a wsd schema to another.
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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32
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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33 -----
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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34
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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35 **Inputs**
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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36
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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37 A xml metadata file using a standard (for exemple EML, ISO19115,...) and a xsl file describing the mapping between the standard terms from input file and terms of the searched output standard.
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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38
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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39 -----
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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40
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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41 **Outputs**
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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42
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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43 A xml metadata file using a new standard (for example ISO19115, EML, ...).
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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44 </help>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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45 <citations>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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46 <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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47 author = {Mikhail Grushinskiy},
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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48 title = {XMLStarlet Command Line XML Toolkit},
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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49 howpublished = "\url{http://xmlstar.sourceforge.net/}",
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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50 year = {2021},
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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51 note = "{online; accessed 08-November-2021}"
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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52 }</citation>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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53 </citations>
217dc3233546 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet commit 6ebe0c98dd0d727b9202422e64f6d5f7697743fb"
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54 </tool>