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annotate flankBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 9f6bd4c9479f
children
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64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
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1 <tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>create new intervals from the flanks of existing intervals</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 flankBed
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11 $pct
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12 $strand
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13 @GENOME_FILE@
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14 -i '$input'
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16 #if $addition.addition_select == 'b':
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17 -b $addition.b
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18 #else:
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19 -l $addition.l
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20 -r $addition.r
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21 #end if
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22 > '$output'
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23 ]]></command>
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24 <inputs>
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25 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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26 <expand macro="input_conditional_genome_file" />
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27 <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
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28 label="Define -l and -r as a fraction of the feature’s length"
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29 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
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30 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
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31 label="Define -l and -r based on strand"
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32 help="For example, if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
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33 <expand macro="addition" />
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34 </inputs>
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35 <outputs>
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36 <data name="output" format_source="input" metadata_source="input" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input" value="a.bed" ftype="bed" />
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41 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
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42 <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/>
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43 <param name="addition|addition_select" value="b"/>
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44 <param name="addition|b" value="5"/>
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45 <output name="output" file="flankBed_result1.bed" ftype="bed" />
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46 </test>
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47 <test>
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48 <param name="input" value="a.bed" ftype="bed" />
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49 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
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50 <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/>
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51 <param name="addition|addition_select" value="lr"/>
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52 <param name="addition|l" value="2"/>
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53 <param name="addition|r" value="3"/>
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54 <output name="output" file="flankBed_result2.bed" ftype="bed" />
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 **What it does**
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60 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
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61
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62 .. image:: $PATH_TO_IMAGES/flank-glyph.png
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64 .. class:: warningmark
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65
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66 In order to prevent creating intervals that violate chromosome boundaries, bedTools flank requires a bedTool genome file defining the length of each chromosome or contig. . This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column.
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67
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68 If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table".
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70 @REFERENCES@
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71 ]]></help>
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72 <expand macro="citations" />
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73 </tool>