annotate getfastaBed.xml @ 37:ce3c7f062223 draft

"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_getfastabed" name="bedtools GetFastaBed" 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>use intervals to extract sequences from 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>
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 #if str($fasta_source.fasta_source_selector) == 'history':
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
10 #set $fasta_file = $fasta_source.fasta
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
11 #else
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 #set $fasta_file = $fasta_source.fasta_id.fields.path
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
13 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14 bedtools getfasta
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 $name
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
16 $tab
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
17 $strand
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
18 $split
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 -fi '$fasta_file'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
20 -bed '$input'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
21 -fo '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
22 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
23 <inputs>
34
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="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
25 <conditional name="fasta_source">
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 name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
27 <option value="history" selected="true">History</option>
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
28 <option value="preloaded">Server indexed files</option>
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
29 </param>
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
30 <when value="history">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
31 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file" />
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
32 </when>
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
33 <when value="preloaded">
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
34 <param name="fasta_id" type="select">
23
13400f3c3ec5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6418f2e58def1a81b3aa7c04cb5dc33decea1a96
iuc
parents: 11
diff changeset
35 <options from_data_table="fasta_indexes" />
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 10
diff changeset
36 </param>
10
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
37 </when>
c78cf6fe3018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents: 4
diff changeset
38 </conditional>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
39 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
40 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
41 <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
42 label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
43 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
44 label="Force strandedness"
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
45 help="If the feature occupies the antisense strand, the sequence will be reverse complemented" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
46 <expand macro="split" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
47 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
48 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
49 <data name="output" format="fasta">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
50 <change_format>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
51 <when input="tab" value="-tab" format="tabular" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
52 </change_format>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
53 </data>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
54 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
55 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
56 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
57 <param name="input" value="nucBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
58 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
59 <param name="tab" value="False" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
60 <param name="split" value="False" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
61 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
62 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
63 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
64 <param name="input" value="nucBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
65 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
66 <param name="tab" value="True" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
67 <param name="split" value="False" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
68 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
69 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
70 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
71 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
72 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
73
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
74 bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “>chrom>:&lt;start>-&lt;end>”.
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
75
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
76 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
77
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
78 .. class:: warningmark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
79
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
80 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
81
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
82 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
83
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
84 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
85 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
86 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
87 </tool>