Mercurial > repos > iuc > bedtools

annotate complementBed.xml @ 37:ce3c7f062223 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 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
author iuc
date Tue, 23 Mar 2021 20:23:14 +0000
parents dde39ba9c031
children 3e38c9b3214f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
1 <tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@">
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>Extract intervals not represented by an interval file</description>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
6 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="stdio" />
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
8 <command><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
9 complementBed
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
10 -i '$input'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
11 -g @GENOME_FILE@
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 > '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
13 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
14 <inputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" 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: 4
diff changeset
16 <expand macro="input_conditional_genome_file" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
17 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
18 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
20 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
21 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
22 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
23 <param name="input" value="a.bed" ftype="bed" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 4
diff changeset
24 <param name="genome_file_opts_selector" value="hist" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
25 <param name="genome" value="mm9_chr1.len" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
26 <output name="output" file="complementBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
27 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
28 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
29 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
30 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
31
26
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents: 25
diff changeset
32 bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input @STD_BEDTOOLS_INPUT_LABEL@ file.
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
33
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
34 .. image:: $PATH_TO_IMAGES/complement-glyph.png
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
35
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
36 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
37 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
38 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
39 </tool>