Mercurial > repos > iuc > bedtools

annotate fisherBed.xml @ 26:95a3b2c25bd1 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 b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
author iuc
date Thu, 26 Apr 2018 17:02:46 -0400
parents a8eabd2838f6
children 4f7a5ccd2ae9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
a8eabd2838f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
iuc
parents: 17
diff changeset
1 <tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
2 <description>calculate Fisher statistic between two feature files</description>
1
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
3 <macros>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
4 <import>macros.xml</import>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
5 </macros>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
6 <expand macro="requirements" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
7 <expand macro="stdio" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
8 <command>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
9 <![CDATA[
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
10 bedtools fisher
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
11 $strand
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
12 $split
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
13 -a '$inputA'
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
14 -b '$inputB'
1
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
15 -f $overlap
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
16 -g @GENOME_FILE@
1
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
17 $reciprocal
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
18 $m
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
19 > '$output'
1
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
20 ]]>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
21 </command>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
22 <inputs>
26
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents: 19
diff changeset
23 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents: 19
diff changeset
24 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
25 <expand macro="input_conditional_genome_file" />
1
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
26 <expand macro="strand2" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
27 <expand macro="split" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
28 <expand macro="overlap" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
29 <expand macro="reciprocal" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
30 <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue=""
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
31 label="Merge overlapping intervals before looking at overlap" help="(-m)" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
32 </inputs>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
33 <outputs>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
34 <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
35 </outputs>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
36 <tests>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
37 <test>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
38 <param name="inputA" value="fisherBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
39 <param name="inputB" value="fisherBed2.bed" ftype="bed" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
40 <param name="genome_file_opts_selector" value="hist" />
1
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
41 <param name="genome" value="fisherBed.len" ftype="tabular" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
42 <output name="output" file="fisherBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
43 </test>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
44 </tests>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
45 <help>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
46 <![CDATA[
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
47 **What it does**
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
48
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
49 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
50
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
51 @REFERENCES@
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
52 ]]>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
53 </help>
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
54 <expand macro="citations" />
82aac94b06c3 Uploaded
iuc
parents:
diff changeset
55 </tool>