Mercurial > repos > bgruening > trim_galore

comparison macros.xml @ 16:cd7e644cae1d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
author bgruening
date Fri, 08 Oct 2021 09:57:52 +0000
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children eefb644655a5
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15:084bbd8ba7b8 16:cd7e644cae1d
1 <macros>
2 <token name="@TOOL_VERSION@">0.6.7</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">trim-galore</requirement>
7 </requirements>
8 </xml>
9 <xml name="xrefs">
10 <xrefs>
11 <xref type="bio.tools">trim_galore</xref>
12 </xrefs>
13 </xml>
14 <xml name="adapter_trimming">
15 <conditional name="trimming">
16 <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
17 <option value="">Automatic detection</option>
18 <option value="--illumina">Illumina universal</option>
19 <option value="--nextera">Nextera transposase</option>
20 <option value="--small_rna">Illumina small RNA adapters</option>
21 <option value="user">User defined adapter sequence</option>
22 </param>
23 <when value=""/>
24 <when value="--illumina"/>
25 <when value="--nextera"/>
26 <when value="--small_rna"/>
27 <when value="user">
28 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
29 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
30 </param>
31 <yield/>
32 </when>
33 </conditional>
34 </xml>
35 <xml name="paired_adapter_trimming">
36 <expand macro="adapter_trimming">
37 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
38 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
39 </param>
40 </expand>
41 <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
42 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
43 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
44 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
45 (--three_prime_clip_R1)</help>
46 </param>
47 <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
48 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
49 adapter/quality trimming has been performed. This may remove some unwanted bias from
50 the 3' end that is not directly related to adapter sequence or basecall quality.</help>
51 </param>
52 </xml>
53 <xml name="citations">
54 <citations>
55 <citation type="bibtex">
56 @misc{githubTrim_Galore,
57 author = {Krueger, Felix},
58 year = {2021},
59 title = {Trim Galore},
60 publisher = {GitHub},
61 journal = {GitHub repository},
62 url = {https://https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye}}
63 </citation>
64 </citations>
65 </xml>
66 </macros>