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annotate shared_macros.xml @ 1:747d464670f9 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit 2727330d0394c8a1f178061abffe91fe621be7ee
author galaxyp
date Fri, 12 Dec 2025 21:10:38 +0000
parents 8184d4998259
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
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1 <macros>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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2 <token name="@TOOL_VERSION@">6.0.2</token>
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747d464670f9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit 2727330d0394c8a1f178061abffe91fe621be7ee
galaxyp
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3 <token name="@VERSION_SUFFIX@">1</token>
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8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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4 <token name="@AA_RE@">[ACDEFGHIKLMNPQRSTVWY]</token>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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5 <token name="@PROBLEM_AA_RE@">(@AA_RE@+|@AA_RE@:-?\d+)</token>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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6 <token name="@PROBLEM_AA_ARG_RE@">@PROBLEM_AA_RE@(,@PROBLEM_AA_RE@)*</token>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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7 <token name="@PREPARE_ALLELES_INPUT@"><![CDATA[
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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8 #if $alleles.allelesrc == 'entry'
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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9 #set $alleles_input = ''
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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10 #if $alleles.allele_text != ''
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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11 #set $alleles_input = ','.join(str($alleles.allele_text).strip().split())
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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12 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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13
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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14 #if $alleles.allele_select != 'None'
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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15 #set $select_alleles = ','.join(str($alleles.allele_select).strip().split())
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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16 #if $alleles_input == ''
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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17 #set $alleles_input = $select_alleles
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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18 #else
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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19 #set $alleles_input = ','.join([$alleles_input, $select_alleles])
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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20 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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21 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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22 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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23 ]]></token>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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24 <xml name="allele_inputs">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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25 <conditional name="alleles">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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26 <param name="allelesrc" type="select" label="Alleles">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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27 <option value="history">From history</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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28 <option value="entry">Entered</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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29 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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30 <when value="history">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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31 <param name="allele_file" type="data" format="txt,tabular,tsv" label="Alleles file">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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32 <help>The dataset should have one allele per line.</help>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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33 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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34 </when>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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35 <when value="entry">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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36 <param name="allele_text" type="text" label="Alleles" optional="true">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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37 <help>Enter alleles separated by white space.</help>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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38 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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39 <expand macro="allele_list" />
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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40 </when>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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41 </conditional>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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42 </xml>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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43 <xml name="citations">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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44 <citations>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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45 <citation type="doi">10.1158/2326-6066.CIR-19-0401</citation>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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46 <yield />
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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47 </citations>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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48 </xml>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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49 </macros>