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comparison nucBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 7a06bb42dbb1
comparison
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49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_nucbed" name="bedtools NucBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@">
2 <description>profile the nucleotide content of intervals in a FASTA file</description> 2 <description>profile the nucleotide content of intervals in a FASTA file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 bedtools nuc
10 bedtools nuc 10 $s
11 $s 11 $seq
12 $seq 12 #if str($pattern):
13 #if str($pattern): 13 -pattern '$pattern'
14 -pattern '$pattern' 14 $C
15 $C 15 #end if
16 #end if 16 -fi '$fasta'
17 -fi '$fasta' 17 -bed '$input'
18 -bed '$input' 18 > '$output'
19 > '$output' 19 ]]></command>
20 ]]>
21 </command>
22 <inputs> 20 <inputs>
23 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 21 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
24 <param format="fasta" name="fasta" type="data" label="FASTA file"/> 22 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
25 23
26 <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue="" 24 <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
27 label="Profile the sequence according to strand" /> 25 label="Profile the sequence according to strand" />
28 <param argument="-seq" type="boolean" checked="false" truevalue="-seq" falsevalue="" 26 <param argument="-seq" type="boolean" truevalue="-seq" falsevalue="" checked="false"
29 label="Print the extracted sequence" /> 27 label="Print the extracted sequence" />
30 <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default"> 28 <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default">
31 <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator> 29 <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator>
32 </param> 30 </param>
33 <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" 31 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false"
34 label="Ignore case when matching -pattern"/> 32 label="Ignore case when matching -pattern"/>
35 </inputs> 33 </inputs>
36 <outputs> 34 <outputs>
37 <data format="tabular" name="output" /> 35 <data name="output" format="tabular" />
38 </outputs> 36 </outputs>
39 <tests> 37 <tests>
40 <test> 38 <test>
41 <param name="input" value="nucBed1.bed" ftype="bed" /> 39 <param name="input" value="nucBed1.bed" ftype="bed" />
42 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> 40 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
54 <param name="seq" value="True" /> 52 <param name="seq" value="True" />
55 <param name="pattern" value="TAC" /> 53 <param name="pattern" value="TAC" />
56 <output name="output" file="nucBed_result3.bed" ftype="tabular" /> 54 <output name="output" file="nucBed_result3.bed" ftype="tabular" />
57 </test> 55 </test>
58 </tests> 56 </tests>
59 <help> 57 <help><![CDATA[
60 <![CDATA[
61 **What it does** 58 **What it does**
62 59
63 Profiles the nucleotide content of intervals in a fasta file. 60 Profiles the nucleotide content of intervals in a fasta file.
64 61
65 @REFERENCES@ 62 @REFERENCES@
66 ]]> 63 ]]></help>
67 </help>
68 <expand macro="citations" /> 64 <expand macro="citations" />
69 </tool> 65 </tool>