Mercurial > repos > iuc > snippy

annotate macros.xml @ 5:f9d3b5a6ef31 draft

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"planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2"
author iuc
date Thu, 12 Sep 2019 12:42:17 -0400
parents 4eb9595bff60
children 493a80c7107e
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="@VERSION@">snippy</requirement>
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5 <yield />
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6 </requirements>
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7 </xml>
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8
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9 <xml name="version_command">
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10 <version_command><![CDATA[snippy --version]]></version_command>
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11 </xml>
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13 <token name="@REFERENCE_SOURCE_FILE@">
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14 <![CDATA[
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15 #if $reference_source.reference_source_selector == 'history'
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16 #if $reference_source.ref_file.is_of_type("fasta")
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17 ln -sf '$reference_source.ref_file' 'ref.fna' &&
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18 #elif $reference_source.ref_file.is_of_type("genbank")
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19 ln -sf '$reference_source.ref_file' 'ref.gbk' &&
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20 #end if
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21 #elif $reference_source.reference_source_selector == 'cached'
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22 ln -sf '$reference_source.ref_file.fields.path' 'ref.fna' &&
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23 #end if]]>
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24 </token>
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25
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26 <token name="@REFERENCE_COMMAND@">
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27 <![CDATA[
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28 #if $reference_source.reference_source_selector == 'history'
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29 #if $reference_source.ref_file.is_of_type("fasta")
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30 --ref 'ref.fna'
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31 #elif $reference_source.ref_file.is_of_type("genbank")
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32 --ref 'ref.gbk'
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33 #end if
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34 #elif $reference_source.reference_source_selector == 'cached'
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35 --ref 'ref.fna'
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36 #end if
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37 ]]>
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38 </token>
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39
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40 <xml name="reference_selector">
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41 <conditional name="reference_source">
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42 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
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43 <option value="cached">Use a built-in genome index</option>
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44 <option value="history">Use a genome from history and build index</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 <validator type="no_options" message="No reference genomes are available" />
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50 </options>
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51 </param>
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52 </when>
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53 <when value="history">
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54 <param name="ref_file" type="data" format="fasta,genbank" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
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55 </when>
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56 </conditional>
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57 </xml>
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58
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59 <token name="@VERSION@">4.4.3</token>
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60
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61 <xml name="citations">
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62 <citations>
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63 <citation type="bibtex">@UNPUBLISHED{Seemann2013,
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64 author = "Seemann T",
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65 title = "snippy: fast bacterial variant calling from NGS reads",
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66 year = "2015",
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67 note = "https://github.com/tseemann/snippy",
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68 url = "https://github.com/tseemann/snippy"}</citation>
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69 </citations>
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70 </xml>
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71 </macros>