Mercurial > repos > iuc > bedtools

annotate groupbyBed.xml @ 59:539958feb49c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author iuc
date Thu, 04 Nov 2021 11:35:06 +0000
parents 1d0a0d6a78b1
children f6c88d2e9ae5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
57
1d0a0d6a78b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 56
diff changeset
1 <tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@" profile="@PROFILE@">
17
a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 8
diff changeset
2 <description>group by common cols and summarize other cols</description>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
3 <macros>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
4 <import>macros.xml</import>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
5 </macros>
59
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
6 <expand macro="bio_tools" />
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
7 <expand macro="requirements" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
8 <expand macro="stdio" />
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
9 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
10 bedtools groupby
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
11 -i '${inputA}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
12 -g '$group'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
13 -c '${cols}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
14 -o $operation
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
15 > '${output}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
16 ]]></command>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
17 <inputs>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
18 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
19 <expand macro="choose_columns" />
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
20 <param name="group" argument="-g" type="text" value="1,2,3"
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
21 label="Specifies which column(s) (1-based) should be used to group the input"
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
22 help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed.">
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
23 <sanitizer invalid_char="">
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
24 <valid initial="string.digits"><add value=","/><add value="-"/></valid>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
25 </sanitizer>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
26 </param>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
27 <param name="operation" argument="-o" type="select" label="Specify the operation">
59
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
28 <!-- <option value="sum" selected="true">Sum - numeric only</option> This is already in math-->
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
29 <option value="stdev">Stdev - numeric only</option>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
30 <option value="sstdev">Sstdev - numeric only</option>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
31 <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
32 <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
33 <option value="first">First - numeric or text</option>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
34 <option value="last">Last - numeric or text</option>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
35 <expand macro="math_options" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
36 <expand macro="additional_math_options" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
37 </param>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
38 </inputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
39 <outputs>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
40 <data name="output" format_source="inputA" metadata_source="inputA"/>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
41 </outputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
42 <tests>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
43 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
44 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
45 <param name="cols" value="9" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
46 <param name="group" value="1,2,3" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
47 <param name="operation" value="sum" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
48 <output name="output" file="groupbyBed_result1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
49 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
50 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
51 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
52 <param name="cols" value="9" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
53 <param name="group" value="1,2,3" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
54 <param name="operation" value="min" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
55 <output name="output" file="groupbyBed_result2.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
56 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
57 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
58 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
59 <param name="cols" value="9" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
60 <param name="group" value="1-4" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
61 <param name="operation" value="median" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
62 <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
63 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
64 </tests>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
65 <help><![CDATA[
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
66 **What it does**
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
67
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
68 Replicate lines in a file based on columns of comma-separated values.
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
69
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
70 @REFERENCES@
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
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
72 <expand macro="citations" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
73 </tool>