Mercurial > repos > iuc > seqtk

annotate seqtk_telo.xml @ 9:4b494533146a draft

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