Mercurial > repos > iuc > bedtools
comparison nucBed.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | 3e38c9b3214f |
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33:87ee588b3d45 | 34:dde39ba9c031 |
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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> |