Mercurial > repos > anton > bamtools
diff bamtools.xml @ 0:2c2200cecea2 draft
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| author | anton |
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| date | Wed, 10 Sep 2014 11:55:26 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools.xml Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,290 @@ +<?xml version="1.0"?> +<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1"> + <description>BAM datasets and perform other transformations</description> + <requirements> + <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + + <command> + ##set up input files + + #for $bam_count, $input_bam in enumerate( $input_bams ): + ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && + ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && + #end for + + #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 + + ##finished setting up inputs + + ##start bamtools commandline + + 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 + + #for $bam_count, $input_bam in enumerate( $input_bams ): + -in "localbam_${bam_count}.bam" + #end for + + + </command> + <inputs> + + <repeat name="input_bams" title="BAM dataset(s) to filter" min="1"> + <param name="input_bam" type="data" format="bam" label="BAM dataset" /> + </repeat> + + <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 as 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="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"> + <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> + </when> + <when value="coverage"> + <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> + </when> + <when value="header"> + <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> + </when> + <when value="merge"> + <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> + </when> + <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="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_bam" 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="output_bam" file="bamtools-convert-pileup.pu" /> + </test> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="analysis_type_selector" value="count"/> + <output name="output_bam" file="bamtools-count.tab" /> + </test> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="analysis_type_selector" value="coverage"/> + <output name="output_bam" file="bamtools-coverage.tab" /> + </test> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="analysis_type_selector" value="header"/> + <output name="output_bam" file="bamtools-header.txt" /> + </test> + </tests> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <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> +</tool>