Mercurial > repos > devteam > fastx_trimmer
comparison fastx_trimmer.xml @ 6:61b4cedc8934 draft
"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
equal
deleted
inserted
replaced
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 |