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comparison seqtk_telo.xml @ 9:4b494533146a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
author iuc
date Sat, 09 Dec 2023 11:14:21 +0000
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8:3da72230c066 9:4b494533146a
1 <?xml version="1.0"?>
2 <tool id="seqtk_telo" name="seqtk_telo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
3 <description>find telomeres</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/>
9 <expand macro="stdio"/>
10 <command><![CDATA[
11 seqtk telo
12 -m '$m'
13 -p '$p'
14 -d '$d'
15 -s '$s'
16 $P
17 '$in_file'
18 > '$default'
19 ]]></command>
20 <inputs>
21 <expand macro="in_faq"/>
22 <param argument="-m" type="text" value="CCCTAA" label="Telomere repeat to search for. Default is vertebrate" />
23 <param argument="-p" type="integer" value="1" label="Penalty for a non-repeat" />
24 <param argument="-d" type="integer" value="2000" label="Maximum drop" />
25 <param argument="-s" type="integer" value="300" label="Minimum score" />
26 <param argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="false" label="Print scoring" />
27 </inputs>
28 <outputs>
29 <data name="default" format="bed" label="${tool.name} on ${on_string}: telomers"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="in_file" value="seqtk_telo.fa"/>
34 <output name="default" file="seqtk_telo.out" ftype="bed"/>
35 </test>
36 <test>
37 <param name="in_file" value="seqtk_telo.fa.gz" ftype="fasta.gz"/>
38 <output name="default" file="seqtk_telogz.out" ftype="bed"/>
39 </test>
40 </tests>
41 <help><![CDATA[
42 **What it does**
43
44 Identifies telomeres using a default vertebrate repeat sequence CCCTAA, or a user supplied one
45
46
47 ::
48
49 Usage: seqtk telo [options] <in.fq>
50 Options:
51 -m STR motif [CCCTAA]
52 -p INT penalty [1]
53 -d INT max drop [2000]
54 -s INT min score [300]
55 -P print scoring
56
57
58 @ATTRIBUTION@
59 ]]></help>
60 <expand macro="citation" />
61 </tool>