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comparison genomeCoverageBed.xml @ 34:dde39ba9c031 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 05:55:48 -0400
parents 4f7a5ccd2ae9
children 3e38c9b3214f
comparison
equal deleted inserted replaced
33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@">
2 <description>compute the coverage over an entire genome</description> 2 <description>compute the coverage over an entire genome</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 genomecov
10 bedtools genomecov 10 @GENOME_FILE_COVERAGE@
11 @GENOME_FILE_COVERAGE@
12 11
13 $split 12 $split
14 $strand 13 $strand
15 14
16 #if str($report.report_select) == "bg": 15 #if str($report.report_select) == "bg":
17 #if $report.zero_regions: 16 #if $report.zero_regions:
18 $report.zero_regions 17 $report.zero_regions
19 #else: 18 #else:
20 -bg 19 -bg
21 #end if 20 #end if
22 21
23 #if str($report.scale): 22 #if str($report.scale):
24 -scale $report.scale 23 -scale $report.scale
25 #end if 24 #end if
26 #else: 25 #else:
27 #if str($report.max): 26 #if str($report.max):
28 -max $report.max 27 -max $report.max
29 #end if 28 #end if
30 #end if 29 #end if
31 $d 30 $d
32 $dz 31 $dz
33 $five 32 $five
34 $three 33 $three
35 34 > '$output'
36 > '$output' 35 ]]></command>
37 ]]>
38 </command>
39 <inputs> 36 <inputs>
40 <conditional name="input_type"> 37 <conditional name="input_type">
41 <param name="input_type_select" type="select" label="Input type"> 38 <param name="input_type_select" type="select" label="Input type">
42 <option value="bed">@STD_BEDTOOLS_INPUT_LABEL@</option> 39 <option value="bed">@STD_BEDTOOLS_INPUT_LABEL@</option>
43 <option value="bam">BAM</option> 40 <option value="bam">BAM</option>
44 </param> 41 </param>
45 <when value="bed"> 42 <when value="bed">
46 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> 43 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
47 <expand macro="input_conditional_genome_file" /> 44 <expand macro="input_conditional_genome_file" />
48 </when> 45 </when>
49 <when value="bam"> 46 <when value="bam">
50 <param format="bam" name="input" type="data" label="BAM file" /> 47 <param name="input" argument="-ibam" type="data" format="bam" label="BAM file" />
51 </when> 48 </when>
52 </conditional> 49 </conditional>
53 <conditional name="report"> 50 <conditional name="report">
54 <param name="report_select" type="select" label="Output type"> 51 <param name="report_select" type="select" label="Output type">
55 <option value="bg" selected="true">BedGraph coverage file</option> 52 <option value="bg" selected="true">BedGraph coverage file</option>
56 <option value="hist">Data suiteable for Histogram</option> 53 <option value="hist">Data suiteable for Histogram</option>
57 </param> 54 </param>
58 <when value="bg"> 55 <when value="bg">
59 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue="" 56 <param name="zero_regions" argument="-bga" type="boolean" truevalue="-bga" falsevalue="" checked="false"
60 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" /> 57 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported" />
61 <param name="scale" type="float" value="1.0" 58 <param argument="-scale" type="float" value="1.0"
62 label="Scale the coverage by a constant factor" 59 label="Scale the coverage by a constant factor"
63 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)" /> 60 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM)." />
64 </when> 61 </when>
65 <when value="hist"> 62 <when value="hist">
66 <param name="max" type="integer" label="Specify max depth" value="0" 63 <param argument="-max" type="integer" value="0" label="Specify max depth"
67 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)" /> 64 help="Combine all positions with a depth >= max into a single bin in the histogram" />
68 </when> 65 </when>
69 </conditional> 66 </conditional>
70 <expand macro="split" /> 67 <expand macro="split" />
71 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> 68 <param argument="-strand" type="select" label="Calculate coverage based on">
72 <option value="">both strands combined</option> 69 <option value="">both strands combined</option>
73 <option value="-strand +">positive strand only</option> 70 <option value="-strand +">positive strand only</option>
74 <option value="-strand -">negative strand only</option> 71 <option value="-strand -">negative strand only</option>
75 </param> 72 </param>
76 73
77 <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue="" 74 <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
78 label="Report the depth at each genome position with 1-based coordinates" help="(-d)" /> 75 label="Report the depth at each genome position with 1-based coordinates" />
79 <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue="" 76 <param argument="-dz" type="boolean" truevalue="-dz" falsevalue="" checked="false"
80 label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" /> 77 label="Report the depth at each genome position with 0-based coordinatess" />
81 <param name="five" type="boolean" checked="False" truevalue="-5" falsevalue="" 78 <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false"
82 label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" /> 79 label="Calculate coverage of 5’ positions" help="Instead of entire interval" />
83 <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue="" 80 <param name="three" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false"
84 label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" /> 81 label="Calculate coverage of 3’ positions" help="Instead of entire interval" />
85 </inputs> 82 </inputs>
86 <outputs> 83 <outputs>
87 <data format="bedgraph" name="output"> 84 <data name="output" format="bedgraph">
88 <change_format> 85 <change_format>
89 <when input="report.report_select" value="hist" format="tabular" /> 86 <when input="report.report_select" value="hist" format="tabular" />
90 </change_format> 87 </change_format>
91 </data> 88 </data>
92 </outputs> 89 </outputs>
98 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" /> 95 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" />
99 <param name="report_select" value="hist" /> 96 <param name="report_select" value="hist" />
100 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> 97 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
101 </test> 98 </test>
102 </tests> 99 </tests>
103 <help> 100 <help><![CDATA[
104 <![CDATA[
105 **What it does** 101 **What it does**
106 102
107 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format. 103 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.
108 104
109 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png 105 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png
166 chr2L 8 995791 23011544 0.0432735 162 chr2L 8 995791 23011544 0.0432735
167 chr2L 9 996398 23011544 0.0432999 163 chr2L 9 996398 23011544 0.0432999
168 164
169 165
170 @REFERENCES@ 166 @REFERENCES@
171 ]]> 167 ]]></help>
172 </help>
173 <expand macro="citations" /> 168 <expand macro="citations" />
174 </tool> 169 </tool>