Mercurial > repos > iuc > seqtk

annotate seqtk_cutN.xml @ 20:8f26884c60b6 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 e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:36:24 +0000
parents 069c8f0695ee
children f2a792351212
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
17
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 16
diff changeset
2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@.1">
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
3 <description>cut sequence at long N</description>
20
8f26884c60b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 17
diff changeset
4 <expand macro="bio_tools"/>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
5 <macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
6 <import>macros.xml</import>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
7 </macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
8 <expand macro="requirements"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
9 <expand macro="stdio"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
10 <command><![CDATA[
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
11 seqtk cutN
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
12 -n $n
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
13 -p $p
33ded39275c3 Uploaded
iuc
parents:
diff changeset
14 $g
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
15 '$in_file'
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
16 @CONDITIONAL_GZIP_OUT@
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
17 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
18 <inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
19 <expand macro="in_faq"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
20 <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
21 <param argument="-p" type="integer" value="10" label="Penalty for a non-N" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
22 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
23 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
24 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
25 <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
26 </outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
27 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
28 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
29 <param name="in_file" value="seqtk_cutn.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
30 <param name="n" value="1"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
31 <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
32 </test>
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
33 <test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
34 <param name="in_file" value="seqtk_cutn.fa.gz" ftype="fasta.gz"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
35 <param name="n" value="1"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
36 <output name="default" file="seqtk_cutn.out.gz" ftype="fasta.gz"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
37 </test>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
38 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
39 <help><![CDATA[
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
40 **What it does**
33ded39275c3 Uploaded
iuc
parents:
diff changeset
41
33ded39275c3 Uploaded
iuc
parents:
diff changeset
42 Splits long sequences with runs of Ns
33ded39275c3 Uploaded
iuc
parents:
diff changeset
43
33ded39275c3 Uploaded
iuc
parents:
diff changeset
44 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
45
33ded39275c3 Uploaded
iuc
parents:
diff changeset
46 >test
33ded39275c3 Uploaded
iuc
parents:
diff changeset
47 AACTGATCGATCGATCGNNNNNNNNNNNACATG
33ded39275c3 Uploaded
iuc
parents:
diff changeset
48
33ded39275c3 Uploaded
iuc
parents:
diff changeset
49 This will be split into the component sequences without the ambiguity.
33ded39275c3 Uploaded
iuc
parents:
diff changeset
50
33ded39275c3 Uploaded
iuc
parents:
diff changeset
51 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
52
33ded39275c3 Uploaded
iuc
parents:
diff changeset
53 >test:1-17
33ded39275c3 Uploaded
iuc
parents:
diff changeset
54 AACTGATCGATCGATCG
33ded39275c3 Uploaded
iuc
parents:
diff changeset
55 >test:29-33
33ded39275c3 Uploaded
iuc
parents:
diff changeset
56 ACATG
33ded39275c3 Uploaded
iuc
parents:
diff changeset
57
33ded39275c3 Uploaded
iuc
parents:
diff changeset
58 @ATTRIBUTION@
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
59 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
60 <expand macro="citation" />
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
61 </tool>