Mercurial > repos > iuc > seqtk
comparison seqtk_telo.xml @ 9:4b494533146a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
author | iuc |
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date | Sat, 09 Dec 2023 11:14:21 +0000 |
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8:3da72230c066 | 9:4b494533146a |
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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> |