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annotate macros.xml @ 14:8251e0ff00f8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
author iuc
date Thu, 04 Aug 2022 06:57:31 +0000
parents f8bd3fca21a6
children 5f0d8f9f311a
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30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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1 <macros>
2
c4ccdd951eb1 "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 -->
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8251e0ff00f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
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3 <token name="@TOOL_VERSION@">2.4.0</token>
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4 <xml name="citations">
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5 <citations>
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6 <citation type="bibtex">@online{nextclade,
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7 title={nextclade},
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8 year = 2021,
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9 url = {https://github.com/nextstrain/nextclade},
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10 urldate = {2021-03-26}
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11 }
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12 </citation>
30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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13 <yield />
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14 </citations>
30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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15 </xml>
30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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17 <!--
30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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18 command
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19 -->
30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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20 <token name="@REF_FASTA@"><![CDATA[
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21 #if $reference_source.reference_source_selector == 'history':
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22 ln -f -s '$reference_source.ref_file' reference.fa &&
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23 #else:
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24 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
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25 #end if
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26 ]]></token>
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27
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8251e0ff00f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
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28 <token name="@QUERY_FASTA@"><![CDATA[
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29 #if $input_fasta.is_of_type('fasta.gz')
8251e0ff00f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
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30 #set $query = 'query.fa.gz'
8251e0ff00f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
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31 #else
8251e0ff00f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
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32 #set $query = 'query.fa'
8251e0ff00f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
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33 #end if
8251e0ff00f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
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34 ln -s '$input_fasta' $query &&
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35 ]]></token>
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30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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36 <!--
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37 inputs
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38 -->
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39
30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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40 <xml name="reference">
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41 <conditional name="reference_source">
30496d58ddc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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42 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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43 <option value="cached">Use a built-in genome</option>
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44 <option value="history">Use a genome from history</option>
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45 </param>
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46 <when value="cached">
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47 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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48 <options from_data_table="all_fasta">
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49 <filter type="sort_by" column="2"/>
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50 </options>
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51 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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52 </param>
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53 </when>
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54 <when value="history">
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55 <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"/>
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56 </when>
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57 </conditional>
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58 </xml>
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59
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60 <!--
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61 help
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62 -->
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63 <token name="@NEXTCLADE@"><![CDATA[
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64 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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65 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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66 ]]></token>
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67
4
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68 </macros>