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comparison bamToBed.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 b4cf5fca8773
comparison
equal deleted inserted replaced
49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@">
2 <description>converter</description> 2 <description>converter</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 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> 7 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
8 </expand> 8 </expand>
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <command> 10 <command><![CDATA[
11 <![CDATA[ 11 #if $input.extension == 'bam' and $option == "-bedpe":
12 samtools sort -n '${input}' ./input &&
13 #else
14 ln -s '${input}' ./input.bam &&
15 #end if
12 16
13 #if $input.extension == 'bam' and $option == "-bedpe": 17 bedtools bamtobed
14 samtools sort -n "${input}" ./input && 18 $option
15 #else 19 $ed_score
16 ln -s "${input}" ./input.bam && 20 $split
17 #end if 21 #if $tag and str($tag).strip():
18 22 -tag '${tag}'
19 bedtools bamtobed 23 #end if
20 $option 24 -i ./input.bam
21 $ed_score 25 > '${output}'
22 $split 26 ]]></command>
23 #if $tag and str($tag).strip():
24 -tag "${tag}"
25 #end if
26 -i ./input.bam
27 > "${output}"
28 ]]>
29 </command>
30 <inputs> 27 <inputs>
31 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/> 28 <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/>
32 <param name="option" type="select" label="What type of BED output would you like"> 29 <param name="option" type="select" label="What type of BED output would you like">
33 <option value="">Create a 6-column BED file</option> 30 <option value="">Create a 6-column BED file</option>
34 <option value="-bed12">Create a full, 12-column "blocked" BED file</option> 31 <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
35 <option value="-bedpe">Create a paired-end, BEDPE format</option> 32 <option value="-bedpe">Create a paired-end, BEDPE format</option>
36 </param> 33 </param>
37 <expand macro="split" /> 34 <expand macro="split" />
38 <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false" 35 <param name="ed_score" argument="-ed" type="boolean" truevalue="-ed" falsevalue="" checked="false"
39 label="Use alignment's edit-distance for BED score" help="(-ed)" /> 36 label="Use alignment's edit-distance for BED score" />
40 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score" 37 <param argument="-tag" type="text" optional="true"
41 help="(-tag)"/> 38 label="Use other NUMERIC BAM alignment tag as the BED score" />
42 </inputs> 39 </inputs>
43 <outputs> 40 <outputs>
44 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> 41 <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED)"/>
45 </outputs> 42 </outputs>
46 <tests> 43 <tests>
47 <test> 44 <test>
48 <param name="input" value="srma_in3.bam" ftype="bam" /> 45 <param name="input" value="srma_in3.bam" ftype="bam" />
49 <param name="option" value="" /> 46 <param name="option" value="" />
55 <param name="option" value="" /> 52 <param name="option" value="" />
56 <param name="tag" value="NM" /> 53 <param name="tag" value="NM" />
57 <output name="output" file="bamToBed_result2.bed" ftype="bed" /> 54 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
58 </test> 55 </test>
59 </tests> 56 </tests>
60 <help> 57 <help><![CDATA[
61 <![CDATA[
62 **What it does** 58 **What it does**
63 59
64 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. 60 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
65 61
66 .. class:: infomark 62 .. class:: infomark
75 71
76 If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0). 72 If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
77 73
78 74
79 @REFERENCES@ 75 @REFERENCES@
80 ]]> 76 ]]></help>
81 </help>
82 <expand macro="citations" /> 77 <expand macro="citations" />
83 </tool> 78 </tool>