Mercurial > repos > iuc > bedtools
annotate groupbyBed.xml @ 48:2f457890d8c8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
| author | iuc |
|---|---|
| date | Tue, 11 Dec 2018 13:59:34 -0500 |
| parents | d279800f4ff9 |
| children | df28283b3778 |
| rev | line source |
|---|---|
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48
2f457890d8c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
42
diff
changeset
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1 <tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@WRAPPER_VERSION@"> |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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2 <description>group by common cols and summarize other cols</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools groupby | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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11 -i "${inputA}" |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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12 -g '$group' |
| 8 | 13 -c "${cols}" |
| 14 -o $operation | |
| 15 > "${output}" | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
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42
d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
26
diff
changeset
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19 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
| 8 | 20 <expand macro="choose_columns" /> |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
21 <param name="group" type="text" value="1,2,3" |
| 8 | 22 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)"> | |
| 24 <sanitizer invalid_char=""> | |
| 25 <valid initial="string.digits"><add value=","/><add value="-"/></valid> | |
| 26 </sanitizer> | |
| 27 </param> | |
| 28 <param name="operation" type="select" label="Specify the operation" help="(-o)"> | |
| 29 <option value="sum" selected="True">Sum - numeric only</option> | |
| 30 <option value="stdev">Stdev - numeric only</option> | |
| 31 <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> | |
| 33 <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> | |
| 35 <option value="last">Last - numeric or text</option> | |
| 36 <expand macro="math_options" /> | |
| 37 <expand macro="additional_math_options" /> | |
| 38 </param> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data format_source="inputA" name="output" metadata_source="inputA"/> | |
| 42 </outputs> | |
| 43 <tests> | |
| 44 <test> | |
| 45 <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> | |
| 46 <param name="cols" value="9" /> | |
| 47 <param name="group" value="1,2,3" /> | |
| 48 <param name="operation" value="sum" /> | |
| 49 <output name="output" file="groupbyBed_result1.bed" ftype="bed" /> | |
| 50 </test> | |
| 51 <test> | |
| 52 <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> | |
| 53 <param name="cols" value="9" /> | |
| 54 <param name="group" value="1,2,3" /> | |
| 55 <param name="operation" value="min" /> | |
| 56 <output name="output" file="groupbyBed_result2.bed" ftype="bed" /> | |
| 57 </test> | |
| 58 <test> | |
| 59 <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> | |
| 60 <param name="cols" value="9" /> | |
| 61 <param name="group" value="1-4" /> | |
| 62 <param name="operation" value="median" /> | |
| 63 <output name="output" file="groupbyBed_result3.bed" ftype="bed" /> | |
| 64 </test> | |
| 65 </tests> | |
| 66 <help> | |
| 67 <![CDATA[ | |
| 68 **What it does** | |
| 69 | |
| 70 Replicate lines in a file based on columns of comma-separated values. | |
| 71 | |
| 72 @REFERENCES@ | |
| 73 ]]> | |
| 74 </help> | |
| 75 <expand macro="citations" /> | |
| 76 </tool> |