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comparison samtools_coverage.xml @ 2:8a477224dfee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
author iuc
date Wed, 31 May 2023 17:15:17 +0000
parents ae36fab06bc2
children c4ff13d2aab3
comparison
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1:ae36fab06bc2 2:8a477224dfee
1 <tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy1" 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 @PREPARE_IDX@ 10 #if $condition_input.input_pooling == "No":
11 @PREPARE_IDX@
12 #else:
13 @PREPARE_IDX_MULTIPLE@
14 #end if
11 samtools coverage 15 samtools coverage
12 16
13 #if $condition_input.input_pooling == "Yes": 17 #if $condition_input.input_pooling == "Yes":
14 ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input] ) } 18 ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input_bams] ) }
15 #else 19 #else
16 '$condition_input.input' 20 '$condition_input.input'
17 #end if 21 #end if
18 22
19 -l $additional_options.min_read_length 23 -l $additional_options.min_read_length
20 -q $additional_options.min_mq 24 -q $additional_options.min_mq
21 -Q $additional_options.min_bq 25 -Q $additional_options.min_bq
22 26
23 #set $filter = $additional_options.required_flags 27 #set $filter = $additional_options.required_flags
24 @FLAGS@ 28 @FLAGS@
25 -rf $flags 29 --rf $flags
26 30
27 #set $filter = $additional_options.skipped_flags 31 #set $filter = $additional_options.skipped_flags
28 @FLAGS@ 32 @FLAGS@
29 -ff $flags 33 --ff $flags
30 34
31 #if $condition_histogram.histogram_select == "yes" 35 #if $condition_histogram.histogram_select == "yes"
32 -m 36 -m
33 -w $condition_histogram.n_bins 37 -w $condition_histogram.n_bins
34 #if $condition_histogram.region != "": 38 #if $condition_histogram.region != "":
43 <param name="input_pooling" type="select" label="Are you pooling bam files?" help="Calculate the coverage for multiple bam files" > 47 <param name="input_pooling" type="select" label="Are you pooling bam files?" help="Calculate the coverage for multiple bam files" >
44 <option value="No" selected="True">No</option> 48 <option value="No" selected="True">No</option>
45 <option value="Yes">Yes</option> 49 <option value="Yes">Yes</option>
46 </param> 50 </param>
47 <when value="No" > 51 <when value="No" >
48 <param name="input" type="data" format="bam" multiple="true" label="BAM file"/> 52 <param name="input" type="data" format="bam" label="BAM file"/>
49 </when> 53 </when>
50 <when value="Yes"> 54 <when value="Yes">
51 <param name="input" type="data" format="bam" multiple="true" label="BAM files to be pooled"/> 55 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM files to be pooled"/>
52 </when> 56 </when>
53 </conditional> 57 </conditional>
54 58
55 <section name="additional_options" title="Additional Options" expanded="true"> 59 <section name="additional_options" title="Additional Options" expanded="true">
56 <param name="min_read_length" argument="-l" type="integer" min="0" value="0" label="Minimum read length" help="Ignore reads shorter than INT base pairs (Default = 0)" /> 60 <param name="min_read_length" argument="-l" type="integer" min="0" value="0" label="Minimum read length" help="Ignore reads shorter than INT base pairs (Default = 0)" />
94 <param name="n_bins" value="50" /> 98 <param name="n_bins" value="50" />
95 <output name="output" file="results_2.txt" ftype="tabular" /> 99 <output name="output" file="results_2.txt" ftype="tabular" />
96 </test> 100 </test>
97 <test> 101 <test>
98 <param name="input_pooling" value="Yes" /> 102 <param name="input_pooling" value="Yes" />
99 <param name="input" value="test_1.bam,test_2.bam" ftype="bam" /> 103 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
100 <param name="histogram_select" value="yes" /> 104 <param name="histogram_select" value="yes" />
101 <param name="n_bins" value="100" /> 105 <param name="n_bins" value="100" />
102 <output name="output" file="results_3.txt" ftype="tabular" /> 106 <output name="output" file="results_3.txt" ftype="tabular" />
103 </test> 107 </test>
104 </tests> 108 </tests>