Mercurial > repos > devteam > bamtools
diff bamtools.xml @ 3:04866f817daa draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
| author | devteam |
|---|---|
| date | Wed, 18 Jan 2017 11:47:11 -0500 |
| parents | ea3fc1adee75 |
| children | 4d343c1f606b |
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--- a/bamtools.xml Wed Nov 11 12:33:26 2015 -0500 +++ b/bamtools.xml Wed Jan 18 11:47:11 2017 -0500 @@ -1,232 +1,193 @@ <?xml version="1.0"?> -<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.2"> - <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}" "localbam_${bam_count}.bam" && - ln -s "${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> - - <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> - - <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="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> +<tool id="bamtools" name="Convert, Merge, Randomize" version="2.4.0"> + <description>BAM datasets and perform other transformations</description> + <requirements> + <requirement type="package" version="2.4.0">bamtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + ##set up input files + #for $bam_count, $input_bam in enumerate( $input_bams ): + ln -s "${input_bam}" "localbam_${bam_count}.bam" && + ln -s "${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 + 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> + <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> + <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> - </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> + <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_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="output_bam" 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="output_bam" 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="output_bam" 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="output_bam" file="bamtools-header.txt" /> - </test> + <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="output_bam" 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="output_bam" 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="output_bam" 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="output_bam" file="bamtools-header.txt" /> + </test> </tests> - - <stdio> - <exit_code range="1:" /> - </stdio> - - <help> + <help> **What is does** @@ -284,8 +245,8 @@ 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> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> </tool>