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comparison getfastaBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 7a06bb42dbb1
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49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@">
2 <description>use intervals to extract sequences from a FASTA file</description> 2 <description>use intervals to extract sequences from a FASTA file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 #if str($fasta_source.fasta_source_selector) == 'history':
10 #if str( $fasta_source.fasta_source_selector ) == 'history': 10 #set $fasta_file = $fasta_source.fasta
11 #set $fasta_file = $fasta_source.fasta 11 #else
12 #else 12 #set $fasta_file = $fasta_source.fasta_id.fields.path
13 #set $fasta_file = $fasta_source.fasta_id.fields.path 13 #end if
14 #end if 14 bedtools getfasta
15 bedtools getfasta 15 $name
16 $name 16 $tab
17 $tab 17 $strand
18 $strand 18 $split
19 $split 19 -fi '$fasta_file'
20 -fi '$fasta_file' 20 -bed '$input'
21 -bed '$input' 21 -fo '$output'
22 -fo '$output' 22 ]]></command>
23 ]]>
24 </command>
25 <inputs> 23 <inputs>
26 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> 24 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
27 <conditional name="fasta_source"> 25 <conditional name="fasta_source">
28 <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file"> 26 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
29 <option value="history" selected="True">History</option> 27 <option value="history" selected="true">History</option>
30 <option value="preloaded">Server indexed files</option> 28 <option value="preloaded">Server indexed files</option>
31 </param> 29 </param>
32 <when value="history"> 30 <when value="history">
33 <param name="fasta" format="fasta" type="data" label="Fasta file" /> 31 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file" />
34 </when> 32 </when>
35 <when value="preloaded"> 33 <when value="preloaded">
36 <param name="fasta_id" type="select"> 34 <param name="fasta_id" type="select">
37 <options from_data_table="fasta_indexes" /> 35 <options from_data_table="fasta_indexes" />
38 </param> 36 </param>
39 </when> 37 </when>
40 </conditional> 38 </conditional>
41 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" 39 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
42 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" 40 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
43 help="(-name)" /> 41 <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
44 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" 42 label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
45 label="Report extract sequences in a tab-delimited format instead of in FASTA format" 43 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
46 help="(-tab)" />
47 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
48 label="Force strandedness" 44 label="Force strandedness"
49 help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" /> 45 help="If the feature occupies the antisense strand, the sequence will be reverse complemented" />
50 <expand macro="split" /> 46 <expand macro="split" />
51 </inputs> 47 </inputs>
52 <outputs> 48 <outputs>
53 <data format="fasta" name="output"> 49 <data name="output" format="fasta">
54 <change_format> 50 <change_format>
55 <when input="tab" value="-tab" format="tabular" /> 51 <when input="tab" value="-tab" format="tabular" />
56 </change_format> 52 </change_format>
57 </data> 53 </data>
58 </outputs> 54 </outputs>
70 <param name="tab" value="True" /> 66 <param name="tab" value="True" />
71 <param name="split" value="False" /> 67 <param name="split" value="False" />
72 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" /> 68 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
73 </test> 69 </test>
74 </tests> 70 </tests>
75 <help> 71 <help><![CDATA[
76 <![CDATA[
77 **What it does** 72 **What it does**
78 73
79 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>”. 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>”.
80 75
81 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png 76 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
85 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file. 80 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
86 81
87 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. 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.
88 83
89 @REFERENCES@ 84 @REFERENCES@
90 ]]> 85 ]]></help>
91 </help>
92 <expand macro="citations" /> 86 <expand macro="citations" />
93 </tool> 87 </tool>