Mercurial > repos > iuc > bedtools
annotate groupbyBed.xml @ 60:36d57dc82aa6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 4046c1da68a09c7a3c275f6fe890ec71470fd74d"
| author | iuc |
|---|---|
| date | Wed, 12 Jan 2022 19:20:20 +0000 |
| parents | 539958feb49c |
| children | f6c88d2e9ae5 |
| rev | line source |
|---|---|
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1d0a0d6a78b1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
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changeset
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1 <tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@" profile="@PROFILE@"> |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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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> | |
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539958feb49c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents:
57
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changeset
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6 <expand macro="bio_tools" /> |
| 8 | 7 <expand macro="requirements" /> |
| 8 <expand macro="stdio" /> | |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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9 <command><![CDATA[ |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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10 bedtools groupby |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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11 -i '${inputA}' |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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12 -g '$group' |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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13 -c '${cols}' |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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14 -o $operation |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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15 > '${output}' |
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df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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16 ]]></command> |
| 8 | 17 <inputs> |
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50
df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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18 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
| 8 | 19 <expand macro="choose_columns" /> |
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50
df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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20 <param name="group" argument="-g" type="text" value="1,2,3" |
| 8 | 21 label="Specifies which column(s) (1-based) should be used to group the input" |
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50
df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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22 help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed."> |
| 8 | 23 <sanitizer invalid_char=""> |
| 24 <valid initial="string.digits"><add value=","/><add value="-"/></valid> | |
| 25 </sanitizer> | |
| 26 </param> | |
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50
df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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27 <param name="operation" argument="-o" type="select" label="Specify the operation"> |
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59
539958feb49c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents:
57
diff
changeset
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28 <!-- <option value="sum" selected="true">Sum - numeric only</option> This is already in math--> |
| 8 | 29 <option value="stdev">Stdev - numeric only</option> |
| 30 <option value="sstdev">Sstdev - numeric only</option> | |
| 31 <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option> | |
| 32 <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option> | |
| 33 <option value="first">First - numeric or text</option> | |
| 34 <option value="last">Last - numeric or text</option> | |
| 35 <expand macro="math_options" /> | |
| 36 <expand macro="additional_math_options" /> | |
| 37 </param> | |
| 38 </inputs> | |
| 39 <outputs> | |
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50
df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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40 <data name="output" format_source="inputA" metadata_source="inputA"/> |
| 8 | 41 </outputs> |
| 42 <tests> | |
| 43 <test> | |
| 44 <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> | |
| 45 <param name="cols" value="9" /> | |
| 46 <param name="group" value="1,2,3" /> | |
| 47 <param name="operation" value="sum" /> | |
| 48 <output name="output" file="groupbyBed_result1.bed" ftype="bed" /> | |
| 49 </test> | |
| 50 <test> | |
| 51 <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> | |
| 52 <param name="cols" value="9" /> | |
| 53 <param name="group" value="1,2,3" /> | |
| 54 <param name="operation" value="min" /> | |
| 55 <output name="output" file="groupbyBed_result2.bed" ftype="bed" /> | |
| 56 </test> | |
| 57 <test> | |
| 58 <param name="inputA" value="groupbyBed1.bed" ftype="bed" /> | |
| 59 <param name="cols" value="9" /> | |
| 60 <param name="group" value="1-4" /> | |
| 61 <param name="operation" value="median" /> | |
| 62 <output name="output" file="groupbyBed_result3.bed" ftype="bed" /> | |
| 63 </test> | |
| 64 </tests> | |
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50
df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
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65 <help><![CDATA[ |
| 8 | 66 **What it does** |
| 67 | |
| 68 Replicate lines in a file based on columns of comma-separated values. | |
| 69 | |
| 70 @REFERENCES@ | |
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50
df28283b3778
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
48
diff
changeset
|
71 ]]></help> |
| 8 | 72 <expand macro="citations" /> |
| 73 </tool> |