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comparison fastx_reverse_complement.xml @ 2:43540312cb76 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:41:59 -0400
parents a710c1b9776b
children 9d06c848a628
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1:a710c1b9776b 2:43540312cb76
1 <tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement"> 1 <tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements> 5 </requirements>
6 <command>zcat -f '$input' | fastx_reverse_complement -v -o $output 6 <command>
7 <![CDATA[
8 zcat -f < '$input' | fastx_reverse_complement -v -o '$output'
7 #if $input.ext == "fastqsanger": 9 #if $input.ext == "fastqsanger":
8 -Q 33 10 -Q 33
9 #end if 11 #end if
10 </command> 12 ]]>
11 <inputs> 13 </command>
12 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" /> 14 <inputs>
13 </inputs> 15 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
14 16 </inputs>
15 <tests> 17 <outputs>
16 <test> 18 <data format_source="input" name="output" metadata_source="input" />
17 <!-- Reverse-complement a FASTA file --> 19 </outputs>
18 <param name="input" value="fastx_rev_comp1.fasta" /> 20 <tests>
19 <output name="output" file="fastx_reverse_complement1.out" /> 21 <test>
20 </test> 22 <!-- Reverse-complement a FASTA file -->
21 <test> 23 <param name="input" value="fastx_rev_comp1.fasta" />
22 <!-- Reverse-complement a FASTQ file --> 24 <output name="output" ftype="fasta" file="fastx_reverse_complement1.out" />
23 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/> 25 </test>
24 <output name="output" file="fastx_reverse_complement2.out" /> 26 <test>
25 </test> 27 <!-- Reverse-complement a FASTQ file -->
26 </tests> 28 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
27 29 <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" />
28 30 </test>
29 <outputs> 31 </tests>
30 <data format="input" name="output" metadata_source="input" /> 32 <help>
31 </outputs>
32
33 <help>
34 **What it does** 33 **What it does**
35 34
36 This tool reverse-complements each sequence in a library. 35 This tool reverse-complements each sequence in a library.
37 If the library is a FASTQ, the quality-scores are also reversed. 36 If the library is a FASTQ, the quality-scores are also reversed.
38 37
39 -------- 38 --------
40 39
41 **Example** 40 **Example**
42 41
43 Input FASTQ file:: 42 Input FASTQ file::
58 ------ 57 ------
59 58
60 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 59 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
61 60
62 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 61 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
63 62 </help>
64 </help>
65 </tool> 63 </tool>