Mercurial > repos > devteam > fastx_trimmer
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 |
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date | Fri, 17 Aug 2018 05:06:06 -0400 |
parents | bbb007a39ac2 |
children | 547e8d00f11c |
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3:bbb007a39ac2 | 4:b98f3fa516a3 |
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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 |