Mercurial > repos > petr-novak > re_utils

comparison fasta_interlacer.xml @ 22:58807b35777a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 11:31:12 +0000
parents c2c69c6090f0
children cab41d23e2a3
comparison
equal deleted inserted replaced
21:f4ed6a65a2ff 22:58807b35777a
1 <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0.3">
2 <description>Join pared reads into single file</description>
3 <required_files>
4 <include type="literal" path="fasta_interlacer.py"/>
5 </required_files>
6 <command>
7 python '$__tool_directory__'/fasta_interlacer.py -a $A -b $B -p $paired -x $single
8 </command>
1 9
2 <tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0"> 10 <inputs>
3 <description> Join pared reads into single file </description> 11 <param format="fasta" type="data" name="A" label="Left-hand mates"/>
4 <command interpreter="python"> 12 <param format="fasta" type="data" name="B" label="Right-hand mates"/>
5 fasta_interlacer.py -a $A -b $B -p $paired -x $single 13 </inputs>
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 14
13 15
14 <outputs> 16 <outputs>
15 <data format="fasta" name="paired" label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/> 17 <data format="fasta" name="paired"
16 <data format="fasta" name="single" label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/> 18 label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>
17 </outputs> 19 <data format="fasta" name="single"
20 label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/>
21 </outputs>
18 22
19 <help> 23 <help>
20 **What it does** 24 **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. 25 This tools joins paired end FASTA reads from separate files, one with the left
22 Last character in identifiers is used to distinguish pairs. 26 mates and one with the right mates, into a single files.
23 27 Last character in identifiers is used to distinguish pairs.
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 28
32 29 **Note !!!**
30 This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy
31 built-in FASTQ interlacer allows different ordering
32 of sequences in both files but this flexibility comes with high memory
33 requirements when large files are used. FASTA interlacer is simple but order of
34 magnitude
35 faster tools which can be used on files where reads are in the same order.
36
37
38 </help>
33 </tool> 39 </tool>