Mercurial > repos > iuc > bedtools
comparison sortBed.xml @ 43:07e8b80f278c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author | iuc |
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date | Fri, 01 Apr 2022 19:02:51 +0000 |
parents | 7ab85ac5f64b |
children | 589e7e57fd6d |
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42:841fb4dc3ab3 | 43:07e8b80f278c |
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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** |