Mercurial > repos > petr-novak > re_utils
comparison fasta_interlacer.xml @ 3:e320ef2d105a draft
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| author | petr-novak |
|---|---|
| date | Thu, 05 Sep 2019 09:04:56 -0400 |
| parents | |
| children | c2c69c6090f0 |
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| 2:ff658cf87f16 | 3:e320ef2d105a |
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| 1 | |
| 2 <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0"> | |
| 3 <description> Join pared reads into single file </description> | |
| 4 <command interpreter="python"> | |
| 5 fasta_interlacer.py -a $A -b $B -p $paired -x $single | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param format="fasta" type="data" name="A" label="Left-hand mates" /> | |
| 10 <param format="fasta" type="data" name="B" label="Right-hand mates" /> | |
| 11 </inputs> | |
| 12 | |
| 13 | |
| 14 <outputs> | |
| 15 <data format="fasta" name="paired" label="interlaced paired reads from datasets ${A.hid} and ${B.hid} "/> | |
| 16 <data format="fasta" name="single" label="reads without available pair reads from datasets ${A.hid} and ${B.hid}"/> | |
| 17 </outputs> | |
| 18 | |
| 19 <help> | |
| 20 **What it does** | |
| 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. | |
| 22 Last character in identifiers is used to distinguish pairs. | |
| 23 | |
| 24 **Note !!!** | |
| 25 This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy built-in FASTQ interlacer allows different ordering | |
| 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 | |
| 27 faster tools which can be used on files where reads are in the same order. | |
| 28 | |
| 29 | |
| 30 </help> | |
| 31 | |
| 32 | |
| 33 </tool> |