Mercurial > repos > iuc > bedtools
view groupbyBed.xml @ 27:a33db97b220c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1ec398a9421f016b852fe59d46961c12321ee5c8
author | iuc |
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date | Tue, 15 May 2018 14:52:10 -0400 |
parents | 95a3b2c25bd1 |
children | 4f7a5ccd2ae9 |
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<tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0"> <description>group by common cols and summarize other cols</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command> <![CDATA[ bedtools groupby -i "${inputA}" -g '$group' -c "${cols}" -o $operation > "${output}" ]]> </command> <inputs> <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> <expand macro="choose_columns" /> <param name="group" type="text" value="1,2,3" label="Specifies which column(s) (1-based) should be used to group the input" help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)"> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=","/><add value="-"/></valid> </sanitizer> </param> <param name="operation" type="select" label="Specify the operation" help="(-o)"> <option value="sum" selected="True">Sum - numeric only</option> <option value="stdev">Stdev - numeric only</option> <option value="sstdev">Sstdev - numeric only</option> <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option> <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option> <option value="first">First - numeric or text</option> <option value="last">Last - numeric or text</option> <expand macro="math_options" /> <expand macro="additional_math_options" /> </param> </inputs> <outputs> <data format_source="inputA" name="output" metadata_source="inputA"/> </outputs> <tests> <test> <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> <param name="cols" value="9" /> <param name="group" value="1,2,3" /> <param name="operation" value="sum" /> <output name="output" file="groupbyBed_result1.bed" ftype="bed" /> </test> <test> <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> <param name="cols" value="9" /> <param name="group" value="1,2,3" /> <param name="operation" value="min" /> <output name="output" file="groupbyBed_result2.bed" ftype="bed" /> </test> <test> <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> <param name="cols" value="9" /> <param name="group" value="1-4" /> <param name="operation" value="median" /> <output name="output" file="groupbyBed_result3.bed" ftype="bed" /> </test> </tests> <help> <![CDATA[ **What it does** Replicate lines in a file based on columns of comma-separated values. @REFERENCES@ ]]> </help> <expand macro="citations" /> </tool>