Mercurial > repos > iuc > seqtk

annotate macros.xml @ 20:8f26884c60b6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:36:24 +0000
parents 36f4c569a594
children f2a792351212
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">seqtk</requirement>
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6 <requirement type="package" version="2.3.4">pigz</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <xml name="bio_tools">
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11 <xrefs>
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12 <xref type="bio.tools">seqtk</xref>
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13 </xrefs>
8f26884c60b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 </xml>
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15 <token name="@TOOL_VERSION@">1.3</token>
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16 <token name="@AWK_VERSION@">4.2.1</token>
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17 <xml name="stdio">
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18 <stdio>
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19 <!-- Anything other than zero is an error -->
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20 <exit_code range="1:"/>
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21 <exit_code range=":-1"/>
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22 <!-- In case the return code has not been set propery check stderr too -->
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23 <regex match="Error:"/>
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24 <regex match="Exception:"/>
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25 </stdio>
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26 </xml>
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27 <xml name="in_fq">
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28 <param name="in_file" type="data" format="fastq,fastq.gz" label="Input FASTQ file"/>
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29 </xml>
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30 <xml name="in_faq">
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31 <param name="in_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file"/>
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32 </xml>
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33 <token name="@CONDITIONAL_GZIP_OUT@"><![CDATA[
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34 #echo "| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_file.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
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35 ]]></token>
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36 <token name="@ATTRIBUTION@"><![CDATA[
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37 **Attribution**
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38
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39 This Galaxy tool relies on the seqtk toolkit from `lh3/seqtk
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40 <https://github.com/lh3/seqtk/>`_, developed by Heng Li at the Broad Institute
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41 ]]></token>
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42 <xml name="citation">
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43 <citations>
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44 </citations>
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45 </xml>
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46 </macros>