Mercurial > repos > iuc > bedtools
comparison annotateBed.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | b28e0cfa7ba1 |
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33:87ee588b3d45 | 34:dde39ba9c031 |
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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> |