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comparison samtools_depth.xml @ 2:2ee8dc1aeda9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:12:22 +0000
parents 44de678a44c4
children 56faa6a57e50
comparison
equal deleted inserted replaced
1:44de678a44c4 2:2ee8dc1aeda9
1 <tool id="samtools_depth" name="Samtools depth" version="@TOOL_VERSION@"> 1 <tool id="samtools_depth" name="Samtools depth" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>compute the depth at each position or region</description> 2 <description>compute the depth at each position or region</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"/>
30 -Q $mapquality 30 -Q $mapquality
31 #end if 31 #end if
32 #for $i in range(len( $input_bams )): 32 #for $i in range(len( $input_bams )):
33 ${i} 33 ${i}
34 #end for 34 #end for
35 #set $filter = $additional_options.required_flags
36 @FLAGS@
37 -g $flags
38 #set $filter = $additional_options.skipped_flags
39 @FLAGS@
40 -G $flags
41 $additional_options.deletions
42 $additional_options.single_read
43 $output_options.header
35 > '${output}' 44 > '${output}'
36 ]]></command> 45 ]]></command>
37 <inputs> 46 <inputs>
38 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" /> 47 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
39 <conditional name="cond_region"> 48 <conditional name="cond_region">
59 <param name="minlength" type="integer" argument="-l" min="0" optional="true" label="Ignore reads shorter than" /> 68 <param name="minlength" type="integer" argument="-l" min="0" optional="true" label="Ignore reads shorter than" />
60 <param name="maxdepth" type="integer" argument="-m" min="0" optional="true" label="Limits the maximum number of considered alignments starting at any sequence position to INT. Note that, the reported depths values might be larger than INT. If 0, depth is set to the maximum integer value, effectively removing any depth limit. (default = 8000)" /> 69 <param name="maxdepth" type="integer" argument="-m" min="0" optional="true" label="Limits the maximum number of considered alignments starting at any sequence position to INT. Note that, the reported depths values might be larger than INT. If 0, depth is set to the maximum integer value, effectively removing any depth limit. (default = 8000)" />
61 70
62 <param name="basequality" type="integer" argument="-q" min="0" optional="true" label="Only count reads with base quality greater than" /> 71 <param name="basequality" type="integer" argument="-q" min="0" optional="true" label="Only count reads with base quality greater than" />
63 <param name="mapquality" type="integer" argument="-Q" min="0" optional="true" label="Only count reads with mapping quality greater than" /> 72 <param name="mapquality" type="integer" argument="-Q" min="0" optional="true" label="Only count reads with mapping quality greater than" />
73
74 <section name="additional_options" title="Additional Filter Options">
75 <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set.">
76 <expand macro="flag_options" />
77 </param>
78
79 <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).">
80 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
81 </param>
82
83 <param name="deletions" type="boolean" argument="-J" truevalue="-J" falsevalue="" checked="false" label="Include reads with deletions in depth computation." />
84 <param name="single_read" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="For the overlapping section of a read pair, count only the bases of a single read." />
85 </section>
86
87 <section name="output_options" title="Output Options" expanded="true">
88 <param name="header" type="boolean" argument="-H" truevalue="-H" falsevalue="" checked="false" label="Print a file header to file." />
89 </section>
90
64 </inputs> 91 </inputs>
65 <outputs> 92 <outputs>
66 <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> 93 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
67 </outputs> 94 </outputs>
68 <tests> 95 <tests>
96 <!-- 1) -->
69 <test> 97 <test>
70 <conditional name="cond_region"> 98 <conditional name="cond_region">
71 <param name="select_region" value="bed"/> 99 <param name="select_region" value="bed"/>
72 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> 100 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
73 </conditional> 101 </conditional>
74 <param name="input_bams" value="eboVir3.bam" ftype="bam" /> 102 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
75 <output name="output" file="samtools_depth_out1.tab" /> 103 <output name="output" file="samtools_depth_out1.tab" />
76 </test> 104 </test>
105 <!-- 2) -->
77 <test> 106 <test>
78 <conditional name="cond_region"> 107 <conditional name="cond_region">
79 <param name="select_region" value="text"/> 108 <param name="select_region" value="text"/>
80 <param name="region" value="eboVir3:500-1500" /> 109 <param name="region" value="eboVir3:500-1500" />
81 </conditional> 110 </conditional>
82 <param name="input_bams" value="eboVir3.bam" ftype="bam" /> 111 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
83 <output name="output" file="samtools_depth_out2.tab" /> 112 <output name="output" file="samtools_depth_out2.tab" />
84 </test> 113 </test>
114 <!-- 3) -->
85 <test> 115 <test>
86 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> 116 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
87 <param name="all" value="-a"/> 117 <param name="all" value="-a"/>
88 <output name="output" file="samtools_depth_out3.tab" /> 118 <output name="output" file="samtools_depth_out3.tab" />
89 </test> 119 </test>
120 <!-- 4) -->
90 <test> 121 <test>
91 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> 122 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
92 <param name="minlength" value="10" /> 123 <param name="minlength" value="10" />
93 <!-- Odd thing: I did not expect values > 4 in the output, but there are ... ? 124 <!-- Odd thing: I did not expect values > 4 in the output, but there are ... ?
94 see https://github.com/samtools/samtools/issues/889 --> 125 see https://github.com/samtools/samtools/issues/889 -->
95 <param name="maxdepth" value="4" /> 126 <param name="maxdepth" value="4" />
96 <param name="basequality" value="11" /> 127 <param name="basequality" value="11" />
97 <param name="mapquality" value="12" /> 128 <param name="mapquality" value="12" />
98 <output name="output" file="samtools_depth_out4.tab" /> 129 <output name="output" file="samtools_depth_out4.tab" />
130 </test>
131 <!-- 5) Testing argument -H -->
132 <test>
133 <conditional name="cond_region">
134 <param name="select_region" value="bed"/>
135 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
136 </conditional>
137 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
138 <param name="header" value="true" />
139 <output name="output" file="samtools_depth_out5.tab" />
140 </test>
141 <!-- 6) Tetsing argument -g -->
142 <test>
143 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
144 <param name="required_flags" value="2,16,64" />
145 <output name="output" file="samtools_depth_out6.tab" />
146 </test>
147 <!-- 7) Tetsing argument -G -->
148 <test>
149 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
150 <param name="skipped_flags" value="2,16,64" />
151 <output name="output" file="samtools_depth_out7.tab" />
99 </test> 152 </test>
100 </tests> 153 </tests>
101 <help> 154 <help>
102 **What it does** 155 **What it does**
103 156