Mercurial > repos > iuc > bedtools

annotate linksBed.xml @ 60:36d57dc82aa6 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 4046c1da68a09c7a3c275f6fe890ec71470fd74d"
author iuc
date Wed, 12 Jan 2022 19:20:20 +0000
parents 539958feb49c
children
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_links" name="bedtools LinksBed" 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>create a HTML page of links to UCSC locations</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 links
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
11 -base '${basename}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
12 -org '${org}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
13 -db '${db}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
14 -i '${input}'
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="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
19 <param name="basename" argument="-base" type="text" value="http://genome.ucsc.edu"
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
20 label="The 'basename' for the UCSC genome browser" />
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
21 <param argument="-org" type="text" value="human" label="Organism name" help="E.g. mouse, human" />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
22 <param argument="-db" type="text" value="hg19" label="The genome build" />
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
23 </inputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
24 <outputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
25 <data name="output" format="html" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
26 </outputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
27 <tests>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
28 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
29 <param name="input" value="linksBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
30 <param name="basename" value="http://genome.ucsc.edu" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
31 <param name="org" value="" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
32 <param name="db" value="" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
33 <output name="output" file="linksBed_result1.html" lines_diff="2" ftype="html" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
34 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
35 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
36 <param name="input" value="linksBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
37 <param name="basename" value="http://genome.ucsc.edu" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
38 <param name="org" value="mouse" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
39 <param name="db" value="mm9" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
40 <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
41 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
42 </tests>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
43 <help><![CDATA[
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
44 **What it does**
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
45
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
46 Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
47
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
48 @REFERENCES@
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
49 ]]></help>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
50 <expand macro="citations" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
51 </tool>