Mercurial > repos > iuc > bedtools
view makeWindowsBed.xml @ 41:7ab85ac5f64b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author | iuc |
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date | Thu, 04 Nov 2021 11:36:55 +0000 |
parents | 3e38c9b3214f |
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<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>make interval windows across a genome</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools" /> <expand macro="requirements" /> <expand macro="stdio" /> <command><![CDATA[ bedtools makewindows #if $type.type_select == 'genome': @GENOME_FILE_MAKEWINDOWS@ #else: -b '$type.input' #end if #if $action.action_select == 'windowsize': -w $action.windowsize #if $action.step_size.step_size_select == 'yes': -s $action.step_size.step_size #end if #else: -n $action.number #end if $sourcename > '$output' ]]></command> <inputs> <conditional name="type"> <param name="type_select" type="select" label="Work with"> <option value="bed" selected="true">Bed File</option> <option value="genome">Genome File</option> </param> <when value="bed"> <param name="input" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> </when> <when value="genome"> <expand macro="input_conditional_genome_file" /> </when> </conditional> <conditional name="action"> <param name="action_select" type="select" label="Work with"> <option value="windowsize" selected="true">Set WindowSize</option> <option value="number">Give Number of Windows</option> </param> <when value="windowsize"> <param name="windowsize" argument="-w" type="integer" value="1" label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows" help="i.e. same number of nucleotide in each window" /> <conditional name="step_size"> <param name="step_size_select" type="select" label="Specify Step size? i.e. how many base pairs to step before creating a new window" help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows)."> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" /> </when> <when value="no" /> </conditional> </when> <when value="number"> <param name="number" argument="-n" type="integer" value="1" label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows" help="I.e. same number of windows, with varying window sizes" /> </when> </conditional> <param name="sourcename" type="select" label="ID Naming Options"> <option value="" selected="true">Default</option> <option value="-i src">use the source interval's name</option> <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option> <option value="-i srcwinnum">use the source interval's name with the window number.</option> </param> </inputs> <outputs> <data name="output" format="bed" /> </outputs> <tests> <test> <param name="type_select" value="genome" /> <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="mm9_chr1.len" ftype="tabular" /> <param name="action_select" value="windowsize" /> <param name="windowsize" value="1000000" /> <output name="output" file="makeWindowBed_result1.bed" ftype="bed" /> </test> <test> <param name="type_select" value="genome" /> <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="mm9_chr1.len" ftype="tabular" /> <param name="action_select" value="windowsize" /> <param name="windowsize" value="1000000" /> <param name="step_size_select" value="yes" /> <param name="step_size" value="50000" /> <output name="output" file="makeWindowBed_result2.bed" ftype="bed" /> </test> <test> <param name="type_select" value="genome" /> <param name="genome_file_opts_selector" value="hist" /> <param name="genome" value="mm9_chr1.len" ftype="tabular" /> <param name="action_select" value="number" /> <param name="number" value="100" /> <output name="output" file="makeWindowBed_result3.bed" ftype="bed" /> </test> <test> <param name="type_select" value="bed" /> <param name="input" value="makeWindowBed1.bed" ftype="bed" /> <param name="action_select" value="number" /> <param name="number" value="15" /> <output name="output" file="makeWindowBed_result4.bed" ftype="bed" /> </test> </tests> <help><![CDATA[ **What it does** Makes adjacent or sliding windows across a genome or BED file. @REFERENCES@ ]]></help> <expand macro="citations" /> </tool>