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comparison samtools_coverage.xml @ 3:c4ff13d2aab3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
author iuc
date Thu, 29 Jun 2023 10:40:07 +0000
parents 8a477224dfee
children
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2:8a477224dfee 3:c4ff13d2aab3
1 <tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>computes the depth at each position or region</description> 2 <description>computes 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"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #if $condition_input.input_pooling == "No": 10 #if $condition_input.input_pooling == "No":
11 #set $input = $condition_input.input
11 @PREPARE_IDX@ 12 @PREPARE_IDX@
12 #else: 13 #else:
14 #set $input_bams = $condition_input.input_bams
13 @PREPARE_IDX_MULTIPLE@ 15 @PREPARE_IDX_MULTIPLE@
14 #end if 16 #end if
15 samtools coverage 17 samtools coverage
16 18
17 #if $condition_input.input_pooling == "Yes": 19 #if $condition_input.input_pooling == "Yes":
18 ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input_bams] ) } 20 ${ ' '.join( [ "'%s'" % $i for $i, $x in enumerate($condition_input.input_bams)]) }
19 #else 21 #else
20 '$condition_input.input' 22 infile
21 #end if 23 #end if
22 24
23 -l $additional_options.min_read_length 25 -l $additional_options.min_read_length
24 -q $additional_options.min_mq 26 -q $additional_options.min_mq
25 -Q $additional_options.min_bq 27 -Q $additional_options.min_bq
30 32
31 #set $filter = $additional_options.skipped_flags 33 #set $filter = $additional_options.skipped_flags
32 @FLAGS@ 34 @FLAGS@
33 --ff $flags 35 --ff $flags
34 36
37 #if $additional_options.region != "":
38 -r '$additional_options.region'
39 #end if
40
35 #if $condition_histogram.histogram_select == "yes" 41 #if $condition_histogram.histogram_select == "yes"
36 -m 42 -m
37 -w $condition_histogram.n_bins 43 -w $condition_histogram.n_bins
38 #if $condition_histogram.region != "":
39 -r '$condition_histogram.region'
40 #end if
41 #end if 44 #end if
42 45
43 -o '$output' 46 -o '$output'
44 ]]></command> 47 ]]></command>
45 <inputs> 48 <inputs>
66 </param> 69 </param>
67 70
68 <param name="skipped_flags" argument="--ff" type="select" multiple="True" label="Exclude reads with any of the following flags set"> 71 <param name="skipped_flags" argument="--ff" type="select" multiple="True" label="Exclude reads with any of the following flags set">
69 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/> 72 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
70 </param> 73 </param>
74 <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." >
75 <sanitizer invalid_char="">
76 <valid initial="string.ascii_letters,string.digits">
77 <add value=":" />
78 <add value="-" />
79 <add value="_" />
80 </valid>
81 </sanitizer>
82 </param>
71 </section> 83 </section>
72 84
73 <conditional name="condition_histogram"> 85 <conditional name="condition_histogram">
74 <param name="histogram_select" argument="-m" type="select" label="Histogram" help="Show histogram instead of tabular output"> 86 <param name="histogram_select" argument="-m" type="select" label="Histogram" help="Show histogram instead of tabular output">
75 <option value="no" selected="true">No</option> 87 <option value="no" selected="true">No</option>
76 <option value="yes">Yes</option> 88 <option value="yes">Yes</option>
77 </param> 89 </param>
78 <when value="yes"> 90 <when value="yes">
79 <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" /> 91 <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" />
80 <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." />
81 </when> 92 </when>
82 <when value="no" /> 93 <when value="no" />
83 </conditional> 94 </conditional>
84 </inputs> 95 </inputs>
85 96
103 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> 114 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
104 <param name="histogram_select" value="yes" /> 115 <param name="histogram_select" value="yes" />
105 <param name="n_bins" value="100" /> 116 <param name="n_bins" value="100" />
106 <output name="output" file="results_3.txt" ftype="tabular" /> 117 <output name="output" file="results_3.txt" ftype="tabular" />
107 </test> 118 </test>
119 <test><!-- test with a region (requires index) -->
120 <param name="input" value="test_1.bam" ftype="bam" />
121 <param name="region" value="ref1" />
122 <output name="output" file="results_4.tabular" ftype="tabular" />
123 </test>
124 <test><!-- test with pooled BAMs and a region -->
125 <param name="input_pooling" value="Yes" />
126 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
127 <param name="region" value="ref2" />
128 <output name="output" file="results_5.tabular" ftype="tabular" />
129 </test>
108 </tests> 130 </tests>
109 <help><![CDATA[ 131 <help><![CDATA[
110 **What it does** 132 **What it does**
111 133
112 This tool runs the ``samtools coverage`` command. 134 This tool runs the ``samtools coverage`` command.