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comparison bamtools.xml @ 6:e4490b16f0d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 29fe5251fcc37a22a1ce479d7a39f5007a4f02ec
author iuc
date Wed, 11 Jan 2023 08:14:24 +0000
parents befc9dad4ca8
children ddb22028b552
comparison
equal deleted inserted replaced
5:befc9dad4ca8 6:e4490b16f0d7
2 <tool id="bamtools" name="Convert, Merge, Randomize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 2 <tool id="bamtools" name="Convert, Merge, Randomize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3 <description>BAM datasets and perform other transformations</description> 3 <description>BAM datasets and perform other transformations</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements">
8 <command detect_errors="exit_code"> 8 <requirement type="package" version="1.16.1">samtools</requirement>
9 <![CDATA[ 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[
10 ##set up input files 11 ##set up input files
11 ln -s '${input_bams}' localbam.bam && 12 ln -s '${input_bams}' localbam.bam &&
12 ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai && 13 ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai &&
13 #if str( $analysis_type.analysis_type_selector ) == 'convert': 14 #if str( $analysis_type.analysis_type_selector ) == 'convert':
14 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup': 15 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':
58 sort 59 sort
59 ${analysis_type.byname} 60 ${analysis_type.byname}
60 -out '$out_file1' 61 -out '$out_file1'
61 #end if 62 #end if
62 -in localbam.bam 63 -in localbam.bam
63 ]]> 64 ]]></command>
64 </command>
65 <inputs> 65 <inputs>
66 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" /> 66 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" />
67 <conditional name="analysis_type"> 67 <conditional name="analysis_type">
68 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool"> 68 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
69 <option value="convert">Convert</option> 69 <option value="convert">Convert</option>