Mercurial > repos > iuc > seqtk

annotate macros.xml @ 19:36f4c569a594 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 35c8480f525d211d5e9996086c60b2c6d4f89146"
author iuc
date Tue, 10 Sep 2019 13:58:18 -0400
parents 069c8f0695ee
children 8f26884c60b6
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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 <token name="@TOOL_VERSION@">1.3</token>
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11 <token name="@AWK_VERSION@">4.2.1</token>
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12 <xml name="stdio">
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13 <stdio>
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14 <!-- Anything other than zero is an error -->
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15 <exit_code range="1:"/>
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16 <exit_code range=":-1"/>
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17 <!-- In case the return code has not been set propery check stderr too -->
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18 <regex match="Error:"/>
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19 <regex match="Exception:"/>
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20 </stdio>
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21 </xml>
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22 <xml name="in_fq">
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23 <param name="in_file" type="data" format="fastq,fastq.gz" label="Input FASTQ file"/>
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24 </xml>
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25 <xml name="in_faq">
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26 <param name="in_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file"/>
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27 </xml>
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28 <token name="@CONDITIONAL_GZIP_OUT@"><![CDATA[
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29 #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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30 ]]></token>
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31 <token name="@ATTRIBUTION@"><![CDATA[
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32 **Attribution**
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33
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34 This Galaxy tool relies on the seqtk toolkit from `lh3/seqtk
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35 <https://github.com/lh3/seqtk/>`_, developed by Heng Li at the Broad Institute
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36 ]]></token>
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37 <xml name="citation">
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38 <citations>
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39 </citations>
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40 </xml>
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41 </macros>