Mercurial > repos > iuc > bedtools
diff makeWindowsBed.xml @ 34:dde39ba9c031 draft
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 | b28e0cfa7ba1 |
line wrap: on
line diff
--- a/makeWindowsBed.xml Mon Dec 17 14:23:31 2018 -0500 +++ b/makeWindowsBed.xml Mon Apr 29 05:55:48 2019 -0400 @@ -1,39 +1,37 @@ -<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@WRAPPER_VERSION@"> +<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@"> <description>make interval windows across a genome</description> <macros> <import>macros.xml</import> </macros> <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 - -s $action.step_size - #end if - $sourcename - > '$output' -]]> - </command> + <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 + -s $action.step_size +#end if +$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="bed" selected="true">Bed File</option> <option value="genome">Genome File</option> </param> <when value="bed"> - <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> + <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" /> @@ -41,11 +39,11 @@ </conditional> <conditional name="action"> <param name="action_select" type="select" label="Work with"> - <option value="windowsize" selected="True">Set WindowSize</option> + <option value="windowsize" selected="true">Set WindowSize</option> <option value="number">Give Number of Windows</option> </param> <when value="windowsize"> - <param name="windowsize" type="integer" value="1" + <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"> @@ -53,23 +51,23 @@ 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> + <option value="no" selected="true">No</option> </param> <when value="yes"> - <param name="step_size" type="integer" value="100" label="Specify it" /> + <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" type="integer" value="1" + <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" /> - <param name="step_size" type="integer" value="100" label="Specify it" /> + help="I.e. same number of windows, with varying window sizes" /> + <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" /> </when> </conditional> <param name="sourcename" type="select" label="ID Naming Options"> - <option value="" selected="True">Default</option> + <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> @@ -115,14 +113,12 @@ <output name="output" file="makeWindowBed_result4.bed" ftype="bed" /> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ **What it does** Makes adjacent or sliding windows across a genome or BED file. @REFERENCES@ -]]> - </help> + ]]></help> <expand macro="citations" /> </tool>