annotate fasta_interlacer.xml @ 20:5a05925340b0 draft

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author petr-novak
date Mon, 07 Jun 2021 08:46:07 +0000
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2 <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0">
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3 <description> Join pared reads into single file </description>
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4 <command interpreter="python">
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5 fasta_interlacer.py -a $A -b $B -p $paired -x $single
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6 </command>
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8 <inputs>
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9 <param format="fasta" type="data" name="A" label="Left-hand mates" />
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10 <param format="fasta" type="data" name="B" label="Right-hand mates" />
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11 </inputs>
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14 <outputs>
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15 <data format="fasta" name="paired" label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>
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16 <data format="fasta" name="single" label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/>
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17 </outputs>
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19 <help>
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20 **What it does**
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21 This tools joins paired end FASTA reads from separate files, one with the left mates and one with the right mates, into a single files.
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22 Last character in identifiers is used to distinguish pairs.
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24 **Note !!!**
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25 This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy built-in FASTQ interlacer allows different ordering
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26 of sequences in both files but this flexibility comes with high memory requirements when large files are used. FASTA interlacer is simple but order of magnitude
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27 faster tools which can be used on files where reads are in the same order.
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30 </help>
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33 </tool>