Mercurial > repos > iuc > nextclade

annotate macros.xml @ 6:1e0234b87809 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 475d00042b5ec4216fa1e5f52e3ec0cf25c67707"
author iuc
date Sat, 25 Sep 2021 18:18:54 +0000
parents 0c46b95d60c3
children f6db3ce6ed1c
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615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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1 <macros>
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
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2 <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools -->
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
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3 <token name="@TOOL_VERSION@">1.3.0</token>
0
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4 <xml name="citations">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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5 <citations>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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6 <citation type="bibtex">@online{nextclade,
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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7 title={nextclade},
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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8 year = 2021,
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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9 url = {https://github.com/nextstrain/nextclade},
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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10 urldate = {2021-03-26}
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11 }
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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12 </citation>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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13 <yield />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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14 </citations>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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15 </xml>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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16
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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17 <!--
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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18 command
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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19 -->
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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20 <token name="@REF_FASTA@"><![CDATA[
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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21 #if $reference_source.reference_source_selector == 'history':
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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22 ln -f -s '$reference_source.ref_file' reference.fa &&
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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23 #else:
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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24 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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25 #end if
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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26 ]]></token>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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27
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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28 <!--
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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29 inputs
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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30 -->
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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31
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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32 <xml name="reference">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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33 <conditional name="reference_source">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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34 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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35 <option value="cached">Use a built-in genome</option>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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36 <option value="history">Use a genome from history</option>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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37 </param>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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38 <when value="cached">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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39 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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40 <options from_data_table="all_fasta">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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41 <filter type="sort_by" column="2"/>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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42 </options>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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43 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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44 </param>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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45 </when>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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46 <when value="history">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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47 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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48 </when>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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49 </conditional>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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50 </xml>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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51
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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52 <!--
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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53 help
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54 -->
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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55 <token name="@NEXTCLADE@"><![CDATA[
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56 Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data.
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57 You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences.
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58 ]]></token>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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59
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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60 </macros>