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comparison fastx_trimmer.xml @ 6:61b4cedc8934 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:31:32 -0500
parents 547e8d00f11c
children 73194cdd4f57
comparison
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5:547e8d00f11c 6:61b4cedc8934
1 <tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences"> 1 <tool id="cshl_fastx_trimmer" version="1.0.2+galaxy0" name="Trim sequences">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements">
7 <requirement type="package" version="1.0.8">bzip2</requirement>
8 </expand>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 @CATS@ fastx_trimmer -v 10 @CATS@ fastx_trimmer -v
9 -f $first 11 -f $first
10 -l $last 12 -l $last
11 -o '$output'
12 @FQQUAL@ 13 @FQQUAL@
13 @GZIP@ 14 @GZIP@
15 > '$output'
14 ]]></command> 16 ]]></command>
15 <inputs> 17 <inputs>
16 <expand macro="fastx_input" /> 18 <expand macro="fastx_input" />
17 <param name="first" type="integer" value="1" label="First base to keep" /> 19 <param name="first" type="integer" value="1" label="First base to keep" />
18 <param name="last" type="integer" value="21" label="Last base to keep" /> 20 <param name="last" type="integer" value="21" label="Last base to keep" />
34 <param name="first" value="1"/> 36 <param name="first" value="1"/>
35 <param name="last" value="27"/> 37 <param name="last" value="27"/>
36 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" /> 38 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
37 </test> 39 </test>
38 <test> 40 <test>
39 <!-- Trim a FASTQ.gz file and output FASTQ.gz --> 41 <!-- Trim a FASTQ.gz file and output FASTQ.gz -->
40 <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/> 42 <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/>
41 <param name="first" value="1"/> 43 <param name="first" value="1"/>
42 <param name="last" value="27"/> 44 <param name="last" value="27"/>
43 <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" /> 45 <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" />
46 </test>
47 <test>
48 <!-- Trim a FASTQ.bz2 file and output FASTQ.bz2 -->
49 <param name="input" value="fastx_trimmer2.fastq.bz2" ftype="fastqsanger.bz2"/>
50 <param name="first" value="1"/>
51 <param name="last" value="27"/>
52 <output name="output" ftype="fastqsanger.bz2" decompress="true" file="fastx_trimmer2.out.bz2" />
44 </test> 53 </test>
45 </tests> 54 </tests>
46 <help><![CDATA[ 55 <help><![CDATA[
47 **What it does** 56 **What it does**
48 57