Mercurial > repos > iuc > cooc_tabmut

annotate macros.xml @ 2:a2963e79f4d7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 1d5ff6cf59878101c2c5c94882d76763b47e169b
author iuc
date Fri, 25 Aug 2023 19:28:56 +0000
parents 74328ad6bb70
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ab84c87e56f7 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"?>
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2 <macros>
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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>
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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/>
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15 </requirements>
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16 </xml>
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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>
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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"
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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.">
74328ad6bb70 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>
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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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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>
ab84c87e56f7 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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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" &&
74328ad6bb70 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
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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>