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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
author | iuc |
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date | Sat, 27 Nov 2021 10:02:03 +0000 |
parents | 4d343c1f606b |
children | e4490b16f0d7 |
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<?xml version="1.0"?> <tool id="bamtools" name="Convert, Merge, Randomize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>BAM datasets and perform other transformations</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ ##set up input files ln -s '${input_bams}' localbam.bam && ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai && #if str( $analysis_type.analysis_type_selector ) == 'convert': #if str( $analysis_type.format_type.format_type_selector ) == 'pileup': #set $reference_fasta_filename = 'localref.fa' #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == 'history': ln -s '${analysis_type.format_type.reference_source.ref_file}' '${reference_fasta_filename}' && samtools faidx '${reference_fasta_filename}' 2>&1 || echo 'Error running samtools faidx for bamtools convert' >&2 && #else: #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path ) #end if #end if #end if bamtools #if str( $analysis_type.analysis_type_selector ) == 'convert': convert -format ${analysis_type.format_type.format_type_selector} #if str( $analysis_type.format_type.format_type_selector ) == 'pileup': ${analysis_type.format_type.mapqual} -fasta '${reference_fasta_filename}' #elif str( $analysis_type.format_type.format_type_selector ) == 'sam': ${analysis_type.format_type.noheader} #end if -out '$out_file1' #elif str( $analysis_type.analysis_type_selector ) == 'count': count > '$out_file1' #elif str( $analysis_type.analysis_type_selector ) == 'coverage': coverage -out '$out_file1' #elif str( $analysis_type.analysis_type_selector ) == 'header': header > '$out_file1' #elif str( $analysis_type.analysis_type_selector ) == 'merge': merge -out '$out_file1' #elif str( $analysis_type.analysis_type_selector ) == 'random': random -n ${analysis_type.count} -seed ${analysis_type.seed} -out '$out_file1' #elif str( $analysis_type.analysis_type_selector ) == 'revert': revert ${analysis_type.keepDuplicate} ${analysis_type.keepQualities} -out '$out_file1' #elif str( $analysis_type.analysis_type_selector ) == 'sort': sort ${analysis_type.byname} -out '$out_file1' #end if -in localbam.bam ]]> </command> <inputs> <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" /> <conditional name="analysis_type"> <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool"> <option value="convert">Convert</option> <option value="count">Count</option> <option value="coverage">Coverage</option> <option value="header">Header</option> <option value="merge">Merge</option> <option value="random">Random</option> <option value="revert">Revert</option> <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. --> <!-- Allowing users for sort files may break donstream functionality. --> <!-- To enable sort option simply uncomment the line below: --> <!-- <option value="sort">Sort</option> --> </param> <when value="convert"> <conditional name="format_type"> <param name="format_type_selector" type="select" help="Select what to convert your BAM to"> <option value="bed">BED</option> <option value="fasta">FASTA</option> <option value="fastq">FASTQ</option> <option value="json">JSON</option> <option value="pileup">Pileup</option> <option value="sam">SAM</option> <option value="yaml">YAML</option> </param> <when value="bed"/> <when value="fasta"/> <when value="fastq"/> <when value="json"/> <when value="yaml"/> <when value="pileup"> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Using reference genome"> <options from_data_table="sam_fa_indexes"> <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <!-- FIX ME!!!! --> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" /> </when> <when value="sam"> <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" /> </when> </conditional> </when> <when value="count" /> <when value="coverage" /> <when value="header" /> <when value="merge" /> <when value="random"> <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" /> <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" /> </when> <when value="revert"> <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" /> <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" /> </when> <!-- <when value="sort"> <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/> </when> --> </conditional> </inputs> <outputs> <data format="txt" name="out_file1"> <change_format> <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" /> <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" /> <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" /> <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" /> <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" /> <when input="analysis_type.analysis_type_selector" value="count" format="tabular" /> <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" /> <when input="analysis_type.analysis_type_selector" value="merge" format="bam" /> <when input="analysis_type.analysis_type_selector" value="random" format="bam" /> <when input="analysis_type.analysis_type_selector" value="revert" format="bam" /> <when input="analysis_type.analysis_type_selector" value="sort" format="bam" /> </change_format> </data> </outputs> <tests> <test> <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="convert"/> <param name="format_type_selector" value="pileup"/> <param name="reference_source_selector" value="history" /> <param name="mapqual" value="true" /> <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/> <output name="out_file1" file="bamtools-convert-pileup.pu" /> </test> <test> <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="count"/> <output name="out_file1" file="bamtools-count.tab" /> </test> <test> <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="coverage"/> <output name="out_file1" file="bamtools-coverage.tab" /> </test> <test> <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="header"/> <output name="out_file1" file="bamtools-header.txt" /> </test> </tests> <help> **What is does** BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below. ----- **Convert** Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either cashed at this Galaxy instance, or provided by you as a FASTA dataset from History. ----- **Count** Counts a number of alignments in a BAM dataset(s). ----- **Coverage** Prints per-base coverage for a BAM dataset. ----- **Header** Prints header from a BAM dataset(s). ------ **Merge** Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button. ------ **Random** Grabs a specified number of random lines from BAM dataset(s). ------ **Revert** Removes duplicate marks and restores original (non-recalibrated) base qualities. ----- .. class:: infomark **More information** Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki </help> <citations> <citation type="doi">10.1093/bioinformatics/btr174</citation> </citations> </tool>