Mercurial > repos > iuc > bedtools

annotate nucBed.xml @ 46:64e2edfe7a2c draft default tip

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 3e7bf5ae62de3520635d75e3825701960b9722e4
author iuc
date Sat, 18 May 2024 23:28:38 +0000
parents 7ab85ac5f64b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 34
diff changeset
1 <tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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>profile the nucleotide content of intervals in a FASTA 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>
41
7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 40
diff changeset
6 <expand macro="bio_tools" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
8 <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
9 <command><![CDATA[
40
a68aa6c1204a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"
iuc
parents: 39
diff changeset
10 ln -s '$fasta' 'input.fasta' &&
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
11 bedtools nuc
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 $s
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
13 $seq
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14 #if str($pattern):
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 -pattern '$pattern'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
16 $C
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
17 #end if
40
a68aa6c1204a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"
iuc
parents: 39
diff changeset
18 -fi 'input.fasta'
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 -bed '$input'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
20 > '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
21 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
22 <inputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
23 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
24 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
25
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
26 <param argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
22
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
27 label="Profile the sequence according to strand" />
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
28 <param argument="-seq" type="boolean" truevalue="-seq" falsevalue="" checked="false"
22
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
29 label="Print the extracted sequence" />
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
30 <param argument="-pattern" type="text" label="Report the number of times a user-defined sequence is observed" help="Case-sensitive by default">
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
31 <validator type="regex" message="Sequence should only contain letters.">^[A-Za-z]*$</validator>
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
32 </param>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
33 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false"
22
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
34 label="Ignore case when matching -pattern"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
35 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
36 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
37 <data name="output" format="tabular" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
38 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
39 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
40 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
41 <param name="input" value="nucBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
42 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
43 <output name="output" file="nucBed_result1.bed" ftype="tabular" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
44 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
45 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
46 <param name="input" value="nucBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
47 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
48 <param name="seq" value="True" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
49 <output name="output" file="nucBed_result2.bed" ftype="tabular" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
50 </test>
22
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
51 <test>
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
52 <param name="input" value="nucBed1.bed" ftype="bed" />
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
53 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
54 <param name="seq" value="True" />
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
55 <param name="pattern" value="TAC" />
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
56 <output name="output" file="nucBed_result3.bed" ftype="tabular" />
bd7721ad15aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c
iuc
parents: 21
diff changeset
57 </test>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
58 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
59 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
60 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
61
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
62 Profiles the nucleotide content of intervals in a fasta file.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
63
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
64 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
65 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
66 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
67 </tool>