Mercurial > repos > iuc > cooc_mutbamscan

annotate macros.xml @ 1:9f1660129403 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
author iuc
date Mon, 31 Jul 2023 15:23:23 +0000
parents 373c1735d31f
children cd0484c5f9f1
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373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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1 <?xml version="1.0"?>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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2 <macros>
1
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3 <token name="@TOOL_VERSION@">0.9</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">21.01</token>
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6 <xml name="biotools">
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7 <xrefs>
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8 <xref type="bio.tools">cojac</xref>
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9 </xrefs>
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10 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">cojac</requirement>
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14 <yield/>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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15 </requirements>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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16 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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17 <xml name="version">
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18 <version_command>echo @TOOL_VERSION@</version_command>
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19 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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20 <xml name="vocdir_input">
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21 <conditional name="voc_source">
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22 <param name="choice" type="select"
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23 label="Source of lineage definitions"
9f1660129403 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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24 help="Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details.">
9f1660129403 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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25 <option value="builtin">Lineage definitions shipped with the tool</option>
9f1660129403 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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26 <option value="custom">YAML dataset collection in history</option>
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27 </param>
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28 <when value="builtin"/>
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373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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29 <when value="custom">
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30 <param name="collection" type="data_collection" collection_type="list" format="yaml" label="Collection of lineage definitions" />
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31 </when>
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32 </conditional>
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33 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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34 <token name="@VOCDIR_COMMAND@"><![CDATA[
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9f1660129403 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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35 #if $voc_config.choice == 'custom'
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36 mkdir -p voc &&
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37 #for $input_file in $voc_config.collection
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38 ln -s '$input_file' 'voc/$input_file.element_identifier' &&
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39 #end for
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40 #else
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41 DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" &&
9f1660129403 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
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42 ln -s "\$DB_PATH" voc &&
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43 #end if
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44 ]]></token>
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45 <token name="@HELP_HEADER@"><![CDATA[
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46 What it does
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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47 ============
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48
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49 The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples.
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50 ]]></token>
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51 <xml name="citations">
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52 <citations>
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53 <citation type="doi">10.1101/2021.01.08.21249379</citation>
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54 </citations>
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55 </xml>
1
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56 </macros>