Mercurial > repos > iuc > seqtk

annotate seqtk_cutN.xml @ 22:f2a792351212 draft default tip

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 75d5141110314addc160504e0a1f9cd66443de66
author iuc
date Wed, 16 Oct 2024 09:08:17 +0000
parents 8f26884c60b6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
f2a792351212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
iuc
parents: 20
diff changeset
1 <tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
2 <description>cut sequence at long N</description>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
3 <macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
4 <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
5 </macros>
22
f2a792351212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
iuc
parents: 20
diff changeset
6 <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
7 <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
8 <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
9 <command><![CDATA[
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
10 seqtk cutN
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
11 -n $n
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
12 -p $p
33ded39275c3 Uploaded
iuc
parents:
diff changeset
13 $g
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
14 '$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
15 @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
16 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
17 <inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
18 <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
19 <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
20 <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
21 <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
22 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
23 <outputs>
22
f2a792351212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
iuc
parents: 20
diff changeset
24 <data name="default" format_source="in_file" label="${tool.name} on ${on_string}: split on N runs longer than $n">
f2a792351212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
iuc
parents: 20
diff changeset
25 <change_format>
f2a792351212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
iuc
parents: 20
diff changeset
26 <when input="g" value="-g" format="bed" />
f2a792351212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
iuc
parents: 20
diff changeset
27 </change_format>
f2a792351212 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
iuc
parents: 20
diff changeset
28 </data>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
29 </outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
30 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
31 <test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
32 <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
33 <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
34 <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
35 </test>
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
36 <test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
37 <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
38 <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
39 <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
40 </test>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
41 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
42 <help><![CDATA[
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
43 **What it does**
33ded39275c3 Uploaded
iuc
parents:
diff changeset
44
33ded39275c3 Uploaded
iuc
parents:
diff changeset
45 Splits long sequences with runs of Ns
33ded39275c3 Uploaded
iuc
parents:
diff changeset
46
33ded39275c3 Uploaded
iuc
parents:
diff changeset
47 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
48
33ded39275c3 Uploaded
iuc
parents:
diff changeset
49 >test
33ded39275c3 Uploaded
iuc
parents:
diff changeset
50 AACTGATCGATCGATCGNNNNNNNNNNNACATG
33ded39275c3 Uploaded
iuc
parents:
diff changeset
51
33ded39275c3 Uploaded
iuc
parents:
diff changeset
52 This will be split into the component sequences without the ambiguity.
33ded39275c3 Uploaded
iuc
parents:
diff changeset
53
33ded39275c3 Uploaded
iuc
parents:
diff changeset
54 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
55
33ded39275c3 Uploaded
iuc
parents:
diff changeset
56 >test:1-17
33ded39275c3 Uploaded
iuc
parents:
diff changeset
57 AACTGATCGATCGATCG
33ded39275c3 Uploaded
iuc
parents:
diff changeset
58 >test:29-33
33ded39275c3 Uploaded
iuc
parents:
diff changeset
59 ACATG
33ded39275c3 Uploaded
iuc
parents:
diff changeset
60
33ded39275c3 Uploaded
iuc
parents:
diff changeset
61 @ATTRIBUTION@
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
62 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
63 <expand macro="citation" />
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
64 </tool>