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comparison groupbyBed.xml @ 34:dde39ba9c031 draft

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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 3e38c9b3214f
comparison
equal deleted inserted replaced
33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@">
2 <description>group by common cols and summarize other cols</description> 2 <description>group by common cols and summarize other cols</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 bedtools groupby
10 bedtools groupby 10 -i '${inputA}'
11 -i "${inputA}" 11 -g '$group'
12 -g '$group' 12 -c '${cols}'
13 -c "${cols}" 13 -o $operation
14 -o $operation 14 > '${output}'
15 > "${output}" 15 ]]></command>
16 ]]>
17 </command>
18 <inputs> 16 <inputs>
19 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 17 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
20 <expand macro="choose_columns" /> 18 <expand macro="choose_columns" />
21 <param name="group" type="text" value="1,2,3" 19 <param name="group" argument="-g" type="text" value="1,2,3"
22 label="Specifies which column(s) (1-based) should be used to group the input" 20 label="Specifies which column(s) (1-based) should be used to group the input"
23 help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)"> 21 help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed.">
24 <sanitizer invalid_char=""> 22 <sanitizer invalid_char="">
25 <valid initial="string.digits"><add value=","/><add value="-"/></valid> 23 <valid initial="string.digits"><add value=","/><add value="-"/></valid>
26 </sanitizer> 24 </sanitizer>
27 </param> 25 </param>
28 <param name="operation" type="select" label="Specify the operation" help="(-o)"> 26 <param name="operation" argument="-o" type="select" label="Specify the operation">
29 <option value="sum" selected="True">Sum - numeric only</option> 27 <option value="sum" selected="true">Sum - numeric only</option>
30 <option value="stdev">Stdev - numeric only</option> 28 <option value="stdev">Stdev - numeric only</option>
31 <option value="sstdev">Sstdev - numeric only</option> 29 <option value="sstdev">Sstdev - numeric only</option>
32 <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option> 30 <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
33 <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option> 31 <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
34 <option value="first">First - numeric or text</option> 32 <option value="first">First - numeric or text</option>
36 <expand macro="math_options" /> 34 <expand macro="math_options" />
37 <expand macro="additional_math_options" /> 35 <expand macro="additional_math_options" />
38 </param> 36 </param>
39 </inputs> 37 </inputs>
40 <outputs> 38 <outputs>
41 <data format_source="inputA" name="output" metadata_source="inputA"/> 39 <data name="output" format_source="inputA" metadata_source="inputA"/>
42 </outputs> 40 </outputs>
43 <tests> 41 <tests>
44 <test> 42 <test>
45 <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> 43 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
46 <param name="cols" value="9" /> 44 <param name="cols" value="9" />
61 <param name="group" value="1-4" /> 59 <param name="group" value="1-4" />
62 <param name="operation" value="median" /> 60 <param name="operation" value="median" />
63 <output name="output" file="groupbyBed_result3.bed" ftype="bed" /> 61 <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
64 </test> 62 </test>
65 </tests> 63 </tests>
66 <help> 64 <help><![CDATA[
67 <![CDATA[
68 **What it does** 65 **What it does**
69 66
70 Replicate lines in a file based on columns of comma-separated values. 67 Replicate lines in a file based on columns of comma-separated values.
71 68
72 @REFERENCES@ 69 @REFERENCES@
73 ]]> 70 ]]></help>
74 </help>
75 <expand macro="citations" /> 71 <expand macro="citations" />
76 </tool> 72 </tool>