Mercurial > repos > iuc > bedtools

comparison sortBed.xml @ 61:9f6bd4c9479f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author iuc
date Fri, 01 Apr 2022 19:00:48 +0000
parents 539958feb49c
children 071c1c5d4bad
comparison
equal deleted inserted replaced
60:36d57dc82aa6 61:9f6bd4c9479f
1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>order the intervals</description> 2 <description>order the intervals</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools" /> 6 <expand macro="bio_tools" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <command><![CDATA[ 9 <command><![CDATA[
10 sortBed 10 sortBed
11 -i '$input' 11 -i '$input'
12 $option 12 $option
13 @GENOME_FILE_MAPBED@ 13 @GENOME_FILE@
14 > '$output' 14 > '$output'
15 ]]></command> 15 ]]></command>
16 <inputs> 16 <inputs>
17 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" /> 17 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" />
18 <param name="option" type="select" label="Sort by"> 18 <param name="option" type="select" label="Sort by">
23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option> 23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option> 24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> 25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> 26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
27 </param> 27 </param>
28 <expand macro="input_optional_genome_file" /> 28 <expand macro="input_conditional_genome_file" help="Sort according to the chromosomes declared in a genome file" />
29 </inputs> 29 </inputs>
30 <outputs> 30 <outputs>
31 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/> 31 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
32 </outputs> 32 </outputs>
33 <tests> 33 <tests>
42 <output name="output" file="sortBed_result2.bed" ftype="bed" /> 42 <output name="output" file="sortBed_result2.bed" ftype="bed" />
43 </test> 43 </test>
44 <test> 44 <test>
45 <param name="input" value="sortBed2.bed" ftype="bed" /> 45 <param name="input" value="sortBed2.bed" ftype="bed" />
46 <param name="option" value="" /> 46 <param name="option" value="" />
47 <param name="genome_choose" value="-g" /> 47 <conditional name="genome_file_opts">
48 <param name="genome_file_opts_selector" value="hist" /> 48 <param name="genome_file_opts_selector" value="hist" />
49 <param name="genome" value="mm9.len" ftype="bed" /> 49 <param name="genome" value="mm9.len" ftype="bed" />
50 </conditional>
50 <output name="output" file="sortBed_result3.bed" ftype="bed" /> 51 <output name="output" file="sortBed_result3.bed" ftype="bed" />
51 </test> 52 </test>
52 </tests> 53 </tests>
53 <help><![CDATA[ 54 <help><![CDATA[
54 **What it does** 55 **What it does**