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comparison fastx_trimmer.xml @ 3:bbb007a39ac2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:28:34 -0400
parents 377ac2829eac
children b98f3fa516a3
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2:377ac2829eac 3:bbb007a39ac2
1 <tool id="cshl_fastx_trimmer" version="1.0.0" name="Trim sequences"> 1 <tool id="cshl_fastx_trimmer" version="1.0.1" name="Trim sequences">
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_trimmer -v -f $first -l $last -o '$output' 8 @CATS@ fastx_trimmer -v
9 #if $input.ext == "fastqsanger": 9 -f $first
10 -Q 33 10 -l $last
11 #end if 11 -o '$output'
12 ]]> 12 @FQQUAL@
13 </command> 13 ]]></command>
14
15 <inputs> 14 <inputs>
16 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" /> 15 <expand macro="fastx_input" />
17 16 <param name="first" type="integer" value="1" label="First base to keep" />
18 <param name="first" type="integer" value="1"> 17 <param name="last" type="integer" value="21" label="Last base to keep" />
19 <label>First base to keep</label>
20 </param>
21
22 <param name="last" type="integer" value="21">
23 <label>Last base to keep</label>
24 </param>
25 </inputs> 18 </inputs>
26 <outputs> 19 <outputs>
27 <data format_source="input" name="output" metadata_source="input" /> 20 <data name="output" format_source="input" metadata_source="input" />
28 </outputs> 21 </outputs>
29 <tests> 22 <tests>
30 <test> 23 <test>
31 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) --> 24 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
32 <param name="input" value="fastx_trimmer1.fasta" /> 25 <param name="input" value="fastx_trimmer1.fasta" />
40 <param name="first" value="1"/> 33 <param name="first" value="1"/>
41 <param name="last" value="27"/> 34 <param name="last" value="27"/>
42 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" /> 35 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
43 </test> 36 </test>
44 </tests> 37 </tests>
45 <help> 38 <help><![CDATA[
46 **What it does** 39 **What it does**
47 40
48 This tool trims (cut bases from) sequences in a FASTA/Q file. 41 This tool trims (cut bases from) sequences in a FASTA/Q file.
49 42
50 -------- 43 --------
55 48
56 >1-1 49 >1-1
57 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC 50 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
58 >2-1 51 >2-1
59 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA 52 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
60
61 53
62 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: 54 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
63 55
64 >1-1 56 >1-1
65 TATGGTCAGAAACCATATGCA 57 TATGGTCAGAAACCATATGCA
76 ------ 68 ------
77 69
78 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
79 71
80 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
81 </help> 73 ]]></help>
74 <expand macro="citations" />
82 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 75 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
83 </tool> 76 </tool>