Mercurial > repos > petr-novak > re_utils
annotate fasta_interlacer.xml @ 29:53dc6aef5441 draft
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author | petr-novak |
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date | Thu, 03 Aug 2023 07:32:40 +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> |
3 | 14 |
15 | |
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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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36 |
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37 |
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38 </help> |
3 | 39 </tool> |