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comparison samtools_bedcov.xml @ 5:540155c5abee draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 15:58:49 +0000
parents b7ab754899d5
children
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4:b7ab754899d5 5:540155c5abee
1 <tool id="samtools_bedcov" name="BedCov" version="2.0.2"> 1 <tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.3" profile="@PROFILE@">
2 <description>calculate read depth for a set of genomic intervals</description> 2 <description>calculate read depth for a set of genomic intervals</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"/>
12 samtools bedcov 12 samtools bedcov
13 #if $mapq: 13 #if $mapq:
14 -Q $mapq 14 -Q $mapq
15 #end if 15 #end if
16 $countdel 16 $countdel
17 #set $filter = $additional_options.required_flags
18 @FLAGS@
19 -g $flags
20 #set $filter = $additional_options.skipped_flags
21 @FLAGS@
22 -G $flags
23 #if $depth_thresh:
24 -d $depth_thresh
25 #end if
17 '${input_bed}' 26 '${input_bed}'
18 #for $i in range(len( $input_bams )): 27 #for $i in range(len($input_bams)):
19 '${i}' 28 '${i}'
20 #end for 29 #end for
21 > '${output}' 30 > '${output}'
22 ]]></command> 31 ]]></command>
23 <inputs> 32 <inputs>
24 <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" /> 33 <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
25 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" /> 34 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
26 <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" /> 35 <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" />
27 <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" /> 36 <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" />
37 <param name="depth_thresh" argument="-d" type="integer" value="" min="0" optional="true" label="Depth threshold" help="Number of reference bases with coverage above and including this value will be displayed in a separate column." />
38
39 <section name="additional_options" title="Additional Filter Options">
40 <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set.">
41 <expand macro="flag_options" />
42 </param>
43
44 <param name="skipped_flags" argument="-G" type="select" multiple="True" label="Exclude reads with any of the following flags set (the default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704).">
45 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
46 </param>
47 </section>
28 </inputs> 48 </inputs>
29 <outputs> 49 <outputs>
30 <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> 50 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
31 </outputs> 51 </outputs>
32 <tests> 52 <tests>
53 <!-- 1) -->
33 <test> 54 <test>
34 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> 55 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
35 <param name="input_bams" value="eboVir3.bam" ftype="bam" /> 56 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
36 <output name="output" file="samtools_bedcov_out1.tab" /> 57 <output name="output" file="samtools_bedcov_out1.tab" />
37 </test> 58 </test>
59 <!-- 2) -->
38 <test> 60 <test>
39 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> 61 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
40 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> 62 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
41 <output name="output" file="samtools_bedcov_out2.tab" /> 63 <output name="output" file="samtools_bedcov_out2.tab" />
42 </test> 64 </test>
65 <!-- 3) -->
43 <test> 66 <test>
44 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> 67 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
45 <param name="input_bams" value="eboVir3.bam" ftype="bam" /> 68 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
46 <param name="mapq" value="40"/> 69 <param name="mapq" value="40"/>
47 <output name="output" file="samtools_bedcov_out1.tab" /> 70 <output name="output" file="samtools_bedcov_out1.tab" />
48 </test> 71 </test>
72 <!-- 4) -->
49 <test> 73 <test>
50 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> 74 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
51 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> 75 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
52 <param name="countdel" value="-j" /> 76 <param name="countdel" value="-j" />
53 <output name="output" file="samtools_bedcov_out2.tab" /> 77 <output name="output" file="samtools_bedcov_out2.tab" />
78 </test>
79 <!-- 5) Testing argument -g -->
80 <test>
81 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
82 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
83 <param name="required_flags" value="2,16,64" />
84 <output name="output" file="samtools_depth_out5.tab" />
85 </test>
86 <!-- 6) Testing argument -G -->
87 <test>
88 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
89 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
90 <param name="skipped_flags" value="2,16,64" />
91 <output name="output" file="samtools_depth_out6.tab" />
92 </test>
93 <!-- 7) Testing depth threshold -d -->
94 <test>
95 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
96 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
97 <param name="depth_thresh" value="10" />
98 <output name="output" file="samtools_bedcov_out7.tab" />
54 </test> 99 </test>
55 </tests> 100 </tests>
56 <help> 101 <help>
57 **What it does** 102 **What it does**
58 103