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comparison fastx_reverse_complement.xml @ 3:3f1017d3f785 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:28:22 -0400
parents e246088b6e34
children 0c2907307ba4
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2:e246088b6e34 3:3f1017d3f785
1 <tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement"> 1 <tool id="cshl_fastx_reverse_complement" version="1.0.1" name="Reverse-Complement">
2 <description></description> 2 <description></description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command> 6 <expand macro="requirements" />
7 <![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 zcat -f < '$input' | fastx_reverse_complement -v -o '$output' 8 @CATS@ fastx_reverse_complement -v
9 #if $input.ext == "fastqsanger": 9 -o '$output'
10 -Q 33 10 @FQQUAL@
11 #end if 11 ]]></command>
12 ]]>
13 </command>
14 <inputs> 12 <inputs>
15 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" /> 13 <expand macro="fastx_input" />
16 </inputs> 14 </inputs>
17 <outputs> 15 <outputs>
18 <data format_source="input" name="output" metadata_source="input" /> 16 <data name="output" format_source="input" metadata_source="input" />
19 </outputs> 17 </outputs>
20 <tests> 18 <tests>
21 <test> 19 <test>
22 <!-- Reverse-complement a FASTA file --> 20 <!-- Reverse-complement a FASTA file -->
23 <param name="input" value="fastx_rev_comp1.fasta" /> 21 <param name="input" value="fastx_rev_comp1.fasta" />
27 <!-- Reverse-complement a FASTQ file --> 25 <!-- Reverse-complement a FASTQ file -->
28 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/> 26 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
29 <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" /> 27 <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" />
30 </test> 28 </test>
31 </tests> 29 </tests>
32 <help> 30 <help><![CDATA[
33 **What it does** 31 **What it does**
34 32
35 This tool reverse-complements each sequence in a library. 33 This tool reverse-complements each sequence in a library.
36 If the library is a FASTQ, the quality-scores are also reversed. 34 If the library is a FASTQ, the quality-scores are also reversed.
37 35
57 ------ 55 ------
58 56
59 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 57 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
60 58
61 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 59 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
62 </help> 60 ]]></help>
61 <expand macro="citations" />
63 </tool> 62 </tool>