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comparison seqtk_cutN.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
comparison
equal deleted inserted replaced
2:f73729b62b51 3:bc7d99f46a5d
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>