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comparison complementBed.xml @ 34:dde39ba9c031 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 05:55:48 -0400
parents 4f7a5ccd2ae9
children 3e38c9b3214f
comparison
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@">
2 <description>Extract intervals not represented by an interval file</description> 2 <description>Extract intervals not represented by an interval 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 complementBed
10 complementBed 10 -i '$input'
11 -i "$input" 11 -g @GENOME_FILE@
12 -g @GENOME_FILE@ 12 > '$output'
13 > "$output" 13 ]]></command>
14 ]]>
15 </command>
16 <inputs> 14 <inputs>
17 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 15 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
18 <expand macro="input_conditional_genome_file" /> 16 <expand macro="input_conditional_genome_file" />
19 </inputs> 17 </inputs>
20 <outputs> 18 <outputs>
21 <data format_source="input" name="output" metadata_source="input" label="Complement of ${input.name}"/> 19 <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
22 </outputs> 20 </outputs>
23 <tests> 21 <tests>
24 <test> 22 <test>
25 <param name="input" value="a.bed" ftype="bed" /> 23 <param name="input" value="a.bed" ftype="bed" />
26 <param name="genome_file_opts_selector" value="hist" /> 24 <param name="genome_file_opts_selector" value="hist" />
27 <param name="genome" value="mm9_chr1.len" /> 25 <param name="genome" value="mm9_chr1.len" />
28 <output name="output" file="complementBed_result1.bed" ftype="bed" /> 26 <output name="output" file="complementBed_result1.bed" ftype="bed" />
29 </test> 27 </test>
30 </tests> 28 </tests>
31 <help> 29 <help><![CDATA[
32 <![CDATA[
33 **What it does** 30 **What it does**
34 31
35 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input @STD_BEDTOOLS_INPUT_LABEL@ file. 32 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input @STD_BEDTOOLS_INPUT_LABEL@ file.
36 33
37 .. image:: $PATH_TO_IMAGES/complement-glyph.png 34 .. image:: $PATH_TO_IMAGES/complement-glyph.png
38 35
39 @REFERENCES@ 36 @REFERENCES@
40 ]]> 37 ]]></help>
41 </help>
42 <expand macro="citations" /> 38 <expand macro="citations" />
43 </tool> 39 </tool>