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comparison annotateBed.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 9a9f1a7abf54
comparison
equal deleted inserted replaced
49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@+galaxy1">
2 <description>annotate coverage of features from multiple files</description> 2 <description>annotate coverage of features from multiple files</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 bedtools annotate
10 -i '${inputA}'
11 #if $names.names_select == 'yes':
12 -files
13 #for $bed in $names.beds:
14 '${bed.input}'
15 #end for
10 16
11 bedtools annotate 17 -names
12 -i "${inputA}" 18 #for $bed in $names.beds:
13 #if $names.names_select == 'yes': 19 '${bed.inputName}'
14 -files 20 #end for
15 #for $bed in $names.beds: 21 #else:
16 "${bed.input}" 22 -files
17 #end for 23 #for $bed in $names.beds:
18 24 '$bed'
19 -names 25 #end for
20 #for $bed in $names.beds: 26 -names
21 "${bed.inputName}" 27 #for $bed in $names.beds:
22 #end for 28 '${bed.display_name}'
23 #else: 29 #end for
24 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] ) 30 #end if
25 -files "${files}" 31 $strand
26 #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] ) 32 $counts
27 -names "${names}" 33 $both
28 #end if 34 > '${output}'
29 $strand 35 ]]></command>
30 $counts
31 $both
32 > "${output}"
33 ]]>
34 </command>
35 <inputs> 36 <inputs>
36 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> 37 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
37 <!-- Additional files, if the user needs more --> 38 <conditional name="names">
38 <conditional name="names">
39 <param name="names_select" type="select" label="Specify names for each file"> 39 <param name="names_select" type="select" label="Specify names for each file">
40 <option value="no" selected="True">No</option> 40 <option value="no" selected="true">No</option>
41 <option value="yes">Yes</option> 41 <option value="yes">Yes</option>
42 </param> 42 </param>
43 <when value="yes"> 43 <when value="yes">
44 <repeat name="beds" title="Add BED files and names" > 44 <repeat name="beds" title="Add BED files and names" >
45 <param name="input" format="bed" type="data" label="BED file" /> 45 <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
46 <param name="inputName" type="text" label="Name of the file" /> 46 <param name="inputName" type="text" label="Name of the file" />
47 </repeat> 47 </repeat>
48 </when> 48 </when>
49 <when value="no"> 49 <when value="no">
50 <param name="beds" format="bed" multiple="True" type="data" label="BED file" /> 50 <param name="beds" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
51 </when> 51 </when>
52 </conditional> 52 </conditional>
53 <expand macro="strand2" /> 53 <expand macro="strand2" />
54 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" 54 <param argument="-counts" type="boolean" truevalue="-counts" falsevalue="" checked="false"
55 label="Report the count of features followed by the % coverage for each annotation file" 55 label="Report the count of features followed by the % coverage for each annotation file"
56 help="Default is to report solely the fraction of -i covered by each file." /> 56 help="Default is to report solely the fraction of -i covered by each file" />
57 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" 57 <param argument="-both" type="boolean" truevalue="-both" falsevalue="" checked="false"
58 label="Report the count of features followed by the % coverage for each annotation file" 58 label="Report the count of features followed by the % coverage for each annotation file"
59 help="Default is to report solely the fraction of the input file covered by each file." /> 59 help="Default is to report solely the fraction of the input file covered by each file" />
60 </inputs> 60 </inputs>
61 <outputs> 61 <outputs>
62 <data format="bed" name="output" /> 62 <data name="output" format="bed" />
63 </outputs> 63 </outputs>
64 <tests> 64 <tests>
65 <test> 65 <test>
66 <param name="inputA" value="annotateBed1.bed" ftype="bed" /> 66 <param name="inputA" value="annotateBed1.bed" ftype="bed" />
67 <param name="names_select" value="no" /> 67 <param name="names_select" value="no" />
68 <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" /> 68 <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" />
69 <output name="output" file="annotateBed_result.bed" ftype="bed" /> 69 <output name="output" file="annotateBed_result.bed" ftype="bed" />
70 </test> 70 </test>
71 </tests> 71 </tests>
72 <help> 72 <help><![CDATA[
73 <![CDATA[
74 **What it does** 73 **What it does**
75 74
76 bedtools annotate, well, annotates one @STD_BEDTOOLS_INPUT_LABEL@ file with the coverage and number of overlaps observed from multiple other @STD_BEDTOOLS_INPUT_LABEL@ files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command. 75 bedtools annotate, well, annotates one @STD_BEDTOOLS_INPUT_LABEL@ file with the coverage and number of overlaps observed from multiple other @STD_BEDTOOLS_INPUT_LABEL@ files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
77 76
78 @REFERENCES@ 77 @REFERENCES@
79 ]]> 78 ]]></help>
80 </help>
81 <expand macro="citations" /> 79 <expand macro="citations" />
82 </tool> 80 </tool>