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annotate fasta_interlacer.xml @ 25:5dba804e6884 draft

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author petr-novak
date Wed, 02 Aug 2023 12:42:08 +0000
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1 <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0.3">
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2 <description>Join pared reads into single file</description>
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3 <required_files>
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4 <include type="literal" path="fasta_interlacer.py"/>
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5 </required_files>
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6 <command>
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7 python '$__tool_directory__'/fasta_interlacer.py -a $A -b $B -p $paired -x $single
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8 </command>
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10 <inputs>
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11 <param format="fasta" type="data" name="A" label="Left-hand mates"/>
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12 <param format="fasta" type="data" name="B" label="Right-hand mates"/>
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13 </inputs>
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16 <outputs>
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17 <data format="fasta" name="paired"
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18 label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>
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19 <data format="fasta" name="single"
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20 label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/>
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21 </outputs>
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23 <help>
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24 **What it does**
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25 This tools joins paired end FASTA reads from separate files, one with the left
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26 mates and one with the right mates, into a single files.
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27 Last character in identifiers is used to distinguish pairs.
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29 **Note !!!**
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30 This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy
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31 built-in FASTQ interlacer allows different ordering
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32 of sequences in both files but this flexibility comes with high memory
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33 requirements when large files are used. FASTA interlacer is simple but order of
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34 magnitude
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35 faster tools which can be used on files where reads are in the same order.
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38 </help>
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39 </tool>