comparison fastx_trimmer.xml @ 4:b98f3fa516a3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
author iuc
date Fri, 17 Aug 2018 05:06:06 -0400
parents bbb007a39ac2
children 547e8d00f11c
comparison
equal deleted inserted replaced
3:bbb007a39ac2 4:b98f3fa516a3
1 <tool id="cshl_fastx_trimmer" version="1.0.1" name="Trim sequences"> 1 <tool id="cshl_fastx_trimmer" version="1.0.2" 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" />
8 @CATS@ fastx_trimmer -v 8 @CATS@ fastx_trimmer -v
9 -f $first 9 -f $first
10 -l $last 10 -l $last
11 -o '$output' 11 -o '$output'
12 @FQQUAL@ 12 @FQQUAL@
13
14 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
15 -z
16 #end if
17
13 ]]></command> 18 ]]></command>
14 <inputs> 19 <inputs>
15 <expand macro="fastx_input" /> 20 <expand macro="fastx_input" />
16 <param name="first" type="integer" value="1" label="First base to keep" /> 21 <param name="first" type="integer" value="1" label="First base to keep" />
17 <param name="last" type="integer" value="21" label="Last base to keep" /> 22 <param name="last" type="integer" value="21" label="Last base to keep" />
31 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) --> 36 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
32 <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/> 37 <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
33 <param name="first" value="1"/> 38 <param name="first" value="1"/>
34 <param name="last" value="27"/> 39 <param name="last" value="27"/>
35 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" /> 40 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
41 </test>
42 <test>
43 <!-- Trim a FASTQ.gz file and output FASTQ.gz -->
44 <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/>
45 <param name="first" value="1"/>
46 <param name="last" value="27"/>
47 <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" />
36 </test> 48 </test>
37 </tests> 49 </tests>
38 <help><![CDATA[ 50 <help><![CDATA[
39 **What it does** 51 **What it does**
40 52