Mercurial > repos > iuc > seqtk
comparison seqtk_cutN.xml @ 3:bc7d99f46a5d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author | iuc |
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date | Mon, 05 Jun 2017 13:27:11 -0400 |
parents | f73729b62b51 |
children | ecf1c30da3a2 |
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2:f73729b62b51 | 3:bc7d99f46a5d |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0"> | 2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0"> |
3 <description>cut sequence at long N</description> | 3 <description>cut sequence at long N</description> |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
9 <command><![CDATA[seqtk cutN -n $n | 9 <command><![CDATA[ |
10 seqtk cutN | |
11 -n $n | |
10 -p $p | 12 -p $p |
11 $g | 13 $g |
12 $in_file | 14 '$in_file' |
13 > $default]]></command> | 15 > '$default' |
14 <inputs> | 16 ]]></command> |
15 <expand macro="in_faq"/> | 17 <inputs> |
16 <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/> | 18 <expand macro="in_faq"/> |
17 <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/> | 19 <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" /> |
18 <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/> | 20 <param argument="-p" type="integer" value="10" label="Penalty for a non-N" /> |
19 </inputs> | 21 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" /> |
20 <outputs> | 22 </inputs> |
21 <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/> | 23 <outputs> |
22 </outputs> | 24 <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/> |
23 <tests> | 25 </outputs> |
24 <test> | 26 <tests> |
25 <param name="in_file" value="seqtk_cutn.fa"/> | 27 <test> |
26 <param name="n" value="1"/> | 28 <param name="in_file" value="seqtk_cutn.fa"/> |
27 <output name="default" file="seqtk_cutn.out" ftype="fasta"/> | 29 <param name="n" value="1"/> |
28 </test> | 30 <output name="default" file="seqtk_cutn.out" ftype="fasta"/> |
29 </tests> | 31 </test> |
30 <help><![CDATA[ | 32 </tests> |
33 <help><![CDATA[ | |
31 **What it does** | 34 **What it does** |
32 | 35 |
33 Splits long sequences with runs of Ns | 36 Splits long sequences with runs of Ns |
34 | 37 |
35 :: | 38 :: |
44 >test:1-17 | 47 >test:1-17 |
45 AACTGATCGATCGATCG | 48 AACTGATCGATCGATCG |
46 >test:29-33 | 49 >test:29-33 |
47 ACATG | 50 ACATG |
48 | 51 |
49 | |
50 @ATTRIBUTION@ | 52 @ATTRIBUTION@ |
51 ]]></help> | 53 ]]></help> |
52 <expand macro="citation" /> | 54 <expand macro="citation" /> |
53 </tool> | 55 </tool> |