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annotate fasta_interlacer.xml @ 32:628b235d76c7 draft

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author petr-novak
date Fri, 04 Aug 2023 07:37:49 +0000
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1 <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0.4">
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2 <description>Join pared reads into single file</description>
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3 <requirements>
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4 <requirement type="package" version="3">python</requirement>
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5 </requirements>
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6 <required_files>
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7 <include type="literal" path="fasta_interlacer.py"/>
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8 </required_files>
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9 <command>
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10 python '$__tool_directory__'/fasta_interlacer.py -a $A -b $B -p $paired -x $single
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11 </command>
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13 <inputs>
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14 <param format="fasta" type="data" name="A" label="Left-hand mates"/>
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15 <param format="fasta" type="data" name="B" label="Right-hand mates"/>
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16 </inputs>
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19 <outputs>
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20 <data format="fasta" name="paired"
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21 label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>
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22 <data format="fasta" name="single"
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23 label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/>
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24 </outputs>
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26 <help>
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27 **What it does**
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28 This tools joins paired end FASTA reads from separate files, one with the left
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29 mates and one with the right mates, into a single files.
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30 Last character in identifiers is used to distinguish pairs.
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32 **Note !!!**
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33 This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy
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34 built-in FASTQ interlacer allows different ordering
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35 of sequences in both files but this flexibility comes with high memory
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36 requirements when large files are used. FASTA interlacer is simple but order of
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37 magnitude
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38 faster tools which can be used on files where reads are in the same order.
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41 </help>
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42 </tool>