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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
author iuc
date Wed, 16 Oct 2024 09:08:17 +0000
parents 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 <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>
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14 </xml>
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15 <token name="@TOOL_VERSION@">1.4</token>
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16 <token name="@VERSION_SUFFIX@">0</token>
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17 <token name="@AWK_VERSION@">4.2.1</token>
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18 <xml name="stdio">
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19 <stdio>
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20 <!-- Anything other than zero is an error -->
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21 <exit_code range="1:"/>
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22 <exit_code range=":-1"/>
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23 <!-- In case the return code has not been set propery check stderr too -->
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24 <regex match="Error:"/>
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25 <regex match="Exception:"/>
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26 </stdio>
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27 </xml>
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28 <xml name="in_fq">
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29 <param name="in_file" type="data" format="fastq,fastq.gz" label="Input FASTQ file"/>
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30 </xml>
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31 <xml name="in_faq">
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32 <param name="in_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file"/>
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33 </xml>
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34 <token name="@CONDITIONAL_GZIP_OUT@"><![CDATA[
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35 #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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36 ]]></token>
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37 <token name="@ATTRIBUTION@"><![CDATA[
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38 **Attribution**
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39
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40 This Galaxy tool relies on the seqtk toolkit from `lh3/seqtk
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41 <https://github.com/lh3/seqtk/>`_, developed by Heng Li at the Broad Institute
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42 ]]></token>
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43 <xml name="citation">
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44 <citations>
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45 <citation type="bibtex">
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46 @misc{seqtk,
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47 author = {Heng Li},
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48 year = {2023},
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49 title = {seqtk},
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50 publisher = {GitHub},
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51 journal = {GitHub repository},
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52 howpublished{\url{https://github.com/lh3/seqtk}},
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53 }
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54 </citation>
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55 </citations>
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56 </xml>
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57
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58 </macros>