Mercurial > repos > anton > bamtools
changeset 0:2c2200cecea2 draft
Uploaded
| author | anton |
|---|---|
| date | Wed, 10 Sep 2014 11:55:26 -0400 |
| parents | |
| children | 2ec7f09c813f |
| files | bamtools-filter.xml bamtools-split.xml bamtools.xml images/complex-filters.png images/multiple-filters.png images/rule.png images/single-filter.png test-data/bamtools-convert-pileup.pu test-data/bamtools-count.tab test-data/bamtools-coverage.tab test-data/bamtools-fasta.fa test-data/bamtools-header.txt test-data/bamtools-input1.bam test-data/bamtools-split-test1.bam test-data/bamtools-test1.bam tool-data/sam_fa_indices.loc.sample tool-data/tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 18 files changed, 5577 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools-filter.xml Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,328 @@ +<tool id="bamFilter" name="Filter" version="0.0.1"> + <description>BAM datasets on a variety of attributes</description> + <requirements> + <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> + </requirements> + <command> + + cat $script_file > $out_file2; + + #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 + + bamtools + filter + -script $script_file + + #for $bam_count, $input_bam in enumerate( $input_bams ): + -in "localbam_${bam_count}.bam" + #end for + -out $out_file1 + + </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> + <repeat name="conditions" title="Condition" min="1"> + <repeat name="filters" title="Filter" min="1"> + <conditional name="bam_property"> + <param name="bam_property_selector" type="select" label="Select BAM property to filter on"> + <option value="alignmentFlag"/> + <option value="cigar"/> + <option value="insertSize"/> + <option value="isDuplicate"/> + <option value="isFailedQC"/> + <option value="isFirstMate"/> + <option value="isMapped"/> + <option value="isMateMapped"/> + <option value="isMateReverseStrand"/> + <option value="isPaired"/> + <option value="isPrimaryAlignment"/> + <option value="isProperPair"/> + <option value="isReverseStrand"/> + <option value="isSecondMate"/> + <option selected="True" value="mapQuality"/> + <option value="matePosition"/> + <option value="mateReference"/> + <option value="name"/> + <option value="position"/> + <option value="queryBases"/> + <option value="reference"/> + <option value="tag"/> + </param> + <!-- would be fanstastic to have AND and OR constructs in when statements --> + <when value="alignmentFlag"> + <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/> + </when> + <when value="cigar"> + <param name="bam_property_value" type="text" size="10" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/> + </when> + <when value="insertSize"> + <param name="bam_property_value" type="text" size="10" value=">=250" label="Filter on inster size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use ">=250""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="isDuplicate"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" /> + </when> + <when value="isFailedQC"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/> + </when> + <when value="isFirstMate"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/> + </when> + <when value="isMapped"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/> + </when> + <when value="isMateMapped"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mapped mate" help="Checked = Mate IS mapped Empty = Mate is NOT mapped"/> + </when> + <when value="isMateReverseStrand"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mate on the reverse strand" help="Checked = Mate IS on reverse strand, Empty = Mate is NOT on the reverse strand"/> + </when> + <when value="isPaired"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select paired reads" help="Checked = Read IS paired, Empty = Read is NOT paired"/> + </when> + <when value="isPrimaryAlignment"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select BAM records for primary alignments" help="Checked = Alignment IS primary, Empty = Alignment is NOT primary"/> + </when> + <when value="isProperPair"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select properly paired reads" help="Checked = Read IS in proper pair, Empty = Read is NOT in the proper pair"/> + </when> + <when value="isReverseStrand"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads in the reverse strand only" help="Checked = Read IS on the reverse strand, Empty = Read is NOT on the reverse strand"/> + </when> + <when value="isSecondMate"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/> + </when> + <when value="mapQuality"> + <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use ">=30""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="matePosition"> + <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use ">1000000""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="mateReference"> + <param name="bam_property_value" type="text" value="chr22" label="Filter on reference name for the mate" help="You can use = and ! (not) in your expression. E.g., to select reads with mates mapping to chrM use "chr22""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="name"> + <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="position"> + <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use ">5000""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="queryBases"> + <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="reference"> + <param name="bam_property_value" type="text" value="chr22" label="Filter on the reference name for the read" help="You can use ! (not) in your expression"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="tag"> + <param name="bam_property_value" type="text" value="NM:>1" label="Filter on a particular tag" help="You can use >, <, =, and ! (not). + Tag name and its value must be separated by ":". E.g., to obtain reads with at least one mismatch use "NM:>1""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value=":!="/></valid> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </repeat> + <conditional name="rule_configuration"> + <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." /> + <when value="true"> + <param name="rules" type="text" size="20" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." > + <sanitizer invalid_char=""> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + </inputs> + + <configfiles> + <configfile name="script_file"> + ##Sets up a json configfile for bamtools filter + ##If there is more than one condition prints brackets and "filters:" + #if len( $conditions ) > 1 + { + "filters": + [ + #end if + #for $i, $c in enumerate( $conditions, start=1 ) + { "id": "$i", + #for $j, $s in enumerate( $c.filters, start=1 ) + ##The if below takes care of the comma at the end of last condition within group + #if $j != len( $c.filters) + "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}", + #else + "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}" + #end if + #end for + ##The if below takes care of the comma at the end of last condition within group + #if $i != len( $conditions ) + }, + #else + } + #end if + #end for + #if len( $conditions ) > 1 + #if str( $rule_configuration.rules_selector ) == "True": + ], + "rule" : "${rule_configuration.rules}" + #else + ] + #end if + } + #end if + </configfile> + </configfiles> + + <outputs> + <data format="txt" name="out_file2" /> + <data format="bam" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="bam_property_selector" value="mapQuality"/> + <param name="bam_property_value" value=">20"/> + <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/> + </test> + </tests> +<help> +**What is does** + +BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). + +----- + +**How it works** + +The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters. + +*Input BAM(s)* + +The input BAM is self-explanatory. This is the dataset you will be filtering. The tool can accept just one or multiple BAM files. To filter on multiple BAMs just add them by clicking **Add new BAM dataset(s) to filter** + +*Conditions and Filters* + +Conditions for filtering BAM files can be arranged in **Groups and Filters**. While it can be confusing at first this is what gives ultimate power to this tools. So try to look at the examples we are supplying below. + +----- + +**Example 1. Using a single filter** + +When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters). +For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below: + +.. image:: ${static_path}/images/simple-filter.png + +----- + +**Example 2. Using multiple filters** + +Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only. +To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button): + +.. image:: ${static_path}/images/multiple-filters.png + +In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering. +In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example. + +----- + +**Example 3. Complex filtering with multiple conditions** + +Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*) +at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*. +The following screenshot expalins how this can be done: + +.. image:: ${static_path}/images/complex-filters.png + +----- + +**Example 4. Even more complex filtering with Rules** + +In the above example we have used two conditions (Condition 1 and Condition 2). Using multiple conditions allows to combine them and a variety of ways to enable even more powerful filtering. +For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such +filtering will look like this:: + + !(1) & (2 | 3) + +Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: + +.. image:: ${static_path}/images/rule.png + +There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule. +Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means:: + + NOT condition 1 AND (condition 2 OR condition 3) + +----- + +**JSON script file** + +This tool produces two outputs. One of the them is a BAM file containing filtered reads. The other is a JSONified script. It can help you to see how your instructions are sent to BAMTools. +For instance, the example 4 looks like this in the JSON form:: + + { + "filters": + [ + { "id": "1", + "tag":"NM:=0", + "isReverseStrand":"false" + }, + { "id": "2", + "tag":"NM:>0", + "isReverseStrand":"true" + } + ] + } + + + +----- + +**More information** + +.. class:: infomark + +Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki + + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools-split.xml Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,116 @@ +<tool id="bamSplit" name="Split" version="0.0.1" force_history_refresh="True"> + <description>BAM datasets on variety of attributes</description> + <requirements> + <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> + </requirements> + <command> + + echo "BAM" > $report && + + #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 + + bamtools + split + + #if str ( $analysis_type.analysis_type_selector ) == "-tag" : + + ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" + + #else + + ${analysis_type.analysis_type_selector} + + #end if + + -stub split_bam + + #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="Split BAM dataset(s) by" help="See help below for explanation of each option"> + <option value="-mapped">Mapping status (-mapped)</option> + <option value="-paired">Pairing status (-paired)</option> + <option value="-reference">Reference name (-reference)</option> + <option value="-tag">Specific tag (-tag)</option> + </param> + <when value="-tag"> + <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> + </when> + </conditional> + </inputs> + + <outputs> + <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> + <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> + </data> + </outputs> + <tests> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="analysis_type_selector" value="-mapped"/> + <output name="report"> + <assert_contents> + <has_line line="BAM" /> + </assert_contents> + <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> + </output> + + </test> + </tests> +<help> +**What is does** + +BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). + +----- + +.. class:: warningmark + +**DANGER: Multiple Outputs** + +As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing. + +----- + +**How it works** + +The following options can be specified via "**Split BAM dataset(s) by**" dropdown:: + + Mapping status (-mapped) split mapped/unmapped and generate two output files + named (MAPPED) and (UNMAPPED) containing mapped and unmapped + reads, respectively. + + Pairing status (-paired) split single-end/paired-end alignments and generate two output files + named (SINGLE_END) and (PAIRED_END) containing paired and unpaired + reads, respectively. + + Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with + very large number of reference sequences (scaffolds) it can generate + thousands (if not millions) of output datasets. + + Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this + option from the menu will allow you to enter the tag name. As was the + case with the reference splitting above, this option can produce very + large number of outputs if a tag has a large number of unique values. + +----- + +.. class:: infomark + +**More information** + +Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki + +</help> +</tool>
--- /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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-convert-pileup.pu Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,239 @@ +phiX174 393 A 1 ^F, h F +phiX174 394 G 1 , < F +phiX174 395 T 1 g ? F +phiX174 396 C 1 , P F +phiX174 397 A 1 , h F +phiX174 398 A 1 , h F +phiX174 399 G 1 , ^ F +phiX174 400 T 1 , H F +phiX174 401 T 1 , h F +phiX174 402 A 1 , V F +phiX174 403 C 1 , h F +phiX174 404 T 1 , E F +phiX174 405 G 1 , P F +phiX174 406 A 1 , h F +phiX174 407 A 1 , h F +phiX174 408 C 1 , h F +phiX174 409 A 1 , h F +phiX174 410 A 1 , h F +phiX174 411 T 1 , h F +phiX174 412 C 1 , h F +phiX174 413 C 1 , h F +phiX174 414 G 1 , O F +phiX174 415 T 1 , G F +phiX174 416 A 1 , ] F +phiX174 417 C 1 , h F +phiX174 418 G 1 , Q F +phiX174 419 T 1 , h F +phiX174 420 T 1 , h F +phiX174 421 T 1 , h F +phiX174 422 C 1 , h F +phiX174 423 C 1 , h F +phiX174 424 A 1 , h F +phiX174 425 G 1 , h F +phiX174 426 A 1 , h F +phiX174 427 C 1 , h F +phiX174 428 C 1 ,$ h F +phiX174 1364 A 1 ^:, h : +phiX174 1365 A 1 , G : +phiX174 1366 G 1 c < : +phiX174 1367 C 1 , h : +phiX174 1368 A 1 , h : +phiX174 1369 T 1 , h : +phiX174 1370 T 1 , S : +phiX174 1371 T 1 , D : +phiX174 1372 G 1 , h : +phiX174 1373 T 1 , H : +phiX174 1374 T 1 , = : +phiX174 1375 T 1 , Q : +phiX174 1376 C 1 , \ : +phiX174 1377 A 1 , h : +phiX174 1378 G 1 , h : +phiX174 1379 G 1 , h : +phiX174 1380 G 1 , h : +phiX174 1381 T 1 , h : +phiX174 1382 T 1 , h : +phiX174 1383 A 1 , h : +phiX174 1384 T 1 , @ : +phiX174 1385 T 1 , J : +phiX174 1386 T 1 g @ : +phiX174 1387 G 1 , R : +phiX174 1388 A 1 , T : +phiX174 1389 A 1 , @ : +phiX174 1390 T 1 , h : +phiX174 1391 A 1 , h : +phiX174 1392 T 1 , h : +phiX174 1393 C 1 , h : +phiX174 1394 T 1 , h : +phiX174 1395 A 1 , h : +phiX174 1396 T 1 , h : +phiX174 1397 A 1 , h : +phiX174 1398 A 1 , h : +phiX174 1399 C 1 ,$ h : +phiX174 2461 G 1 ^:. h : +phiX174 2462 T 1 . h : +phiX174 2463 T 1 . h : +phiX174 2464 A 1 . h : +phiX174 2465 C 1 . h : +phiX174 2466 T 1 . h : +phiX174 2467 C 1 . h : +phiX174 2468 C 1 . h : +phiX174 2469 A 1 . h : +phiX174 2470 G 1 . h : +phiX174 2471 C 1 A ? : +phiX174 2472 T 1 . U : +phiX174 2473 T 1 . [ : +phiX174 2474 C 1 . L : +phiX174 2475 T 1 . W : +phiX174 2476 T 1 . b : +phiX174 2477 C 1 . h : +phiX174 2478 G 1 . h : +phiX174 2479 G 1 . h : +phiX174 2480 C 1 . h : +phiX174 2481 A 1 . h : +phiX174 2482 C 1 . h : +phiX174 2483 C 1 . h : +phiX174 2484 T 1 . L : +phiX174 2485 G 1 . ^ : +phiX174 2486 T 1 . P : +phiX174 2487 T 1 . = : +phiX174 2488 T 1 . h : +phiX174 2489 T 1 . H : +phiX174 2490 A 1 . h : +phiX174 2491 C 1 . h : +phiX174 2492 A 1 . P : +phiX174 2493 G 1 . N : +phiX174 2494 A 1 G = : +phiX174 2495 C 1 . C : +phiX174 2496 A 1 .$ c : +phiX174 4233 G 1 ^:. h : +phiX174 4234 A 1 . \ : +phiX174 4235 T 1 . h : +phiX174 4236 G 1 . h : +phiX174 4237 A 1 . h : +phiX174 4238 G 1 . h : +phiX174 4239 T 1 . h : +phiX174 4240 T 1 . h : +phiX174 4241 T 1 . h : +phiX174 4242 G 1 . h : +phiX174 4243 T 1 C @ : +phiX174 4244 A 1 . N : +phiX174 4245 T 1 . h : +phiX174 4246 C 1 . C : +phiX174 4247 T 1 . Q : +phiX174 4248 G 1 . h : +phiX174 4249 T 1 . h : +phiX174 4250 T 1 . h : +phiX174 4251 A 1 . h : +phiX174 4252 C 1 . h : +phiX174 4253 T 1 . h : +phiX174 4254 G 1 . h : +phiX174 4255 A 1 . h : +phiX174 4256 G 2 .^F. hh :F +phiX174 4257 A 2 G. =V :F +phiX174 4258 A 2 .. CN :F +phiX174 4259 G 2 .. _h :F +phiX174 4260 T 2 .. hh :F +phiX174 4261 T 2 .. Rh :F +phiX174 4262 A 2 .. hh :F +phiX174 4263 A 2 .. hh :F +phiX174 4264 T 2 .. hh :F +phiX174 4265 G 2 .. hh :F +phiX174 4266 G 2 .. UP :F +phiX174 4267 A 2 .. @C :F +phiX174 4268 T 2 .$. hh :F +phiX174 4269 G 1 . [ F +phiX174 4270 A 1 . H F +phiX174 4271 A 1 . N F +phiX174 4272 T 1 . h F +phiX174 4273 T 1 . h F +phiX174 4274 G 1 . h F +phiX174 4275 G 1 . h F +phiX174 4276 C 1 . h F +phiX174 4277 A 1 . h F +phiX174 4278 C 1 . h F +phiX174 4279 A 1 . ? F +phiX174 4280 A 1 . N F +phiX174 4281 T 1 . I F +phiX174 4282 G 1 . c F +phiX174 4283 C 1 . h F +phiX174 4284 T 1 . F F +phiX174 4285 A 1 . ] F +phiX174 4286 C 1 . h F +phiX174 4287 A 1 . g F +phiX174 4288 A 1 . X F +phiX174 4289 T 1 G > F +phiX174 4290 G 1 . V F +phiX174 4291 T 1 .$ h F +phiX174 4724 G 1 ^F. h F +phiX174 4725 T 1 . h F +phiX174 4726 A 1 . E F +phiX174 4727 T 1 . h F +phiX174 4728 T 1 . h F +phiX174 4729 T 1 . h F +phiX174 4730 T 1 . h F +phiX174 4731 T 1 . h F +phiX174 4732 G 1 . h F +phiX174 4733 T 1 . h F +phiX174 4734 G 1 . C F +phiX174 4735 T 1 . R F +phiX174 4736 G 1 . h F +phiX174 4737 C 1 . @ F +phiX174 4738 C 1 . C F +phiX174 4739 T 1 . h F +phiX174 4740 G 1 . h F +phiX174 4741 A 1 . h F +phiX174 4742 G 1 . h F +phiX174 4743 T 1 . h F +phiX174 4744 A 1 . h F +phiX174 4745 T 1 . h F +phiX174 4746 G 1 . h F +phiX174 4747 G 1 . L F +phiX174 4748 T 1 . @ F +phiX174 4749 A 1 . K F +phiX174 4750 C 1 . = F +phiX174 4751 A 1 . G F +phiX174 4752 G 1 . ] F +phiX174 4753 C 1 . h F +phiX174 4754 T 1 . h F +phiX174 4755 A 1 . h F +phiX174 4756 A 1 . J F +phiX174 4757 T 1 . < F +phiX174 4758 G 1 . T F +phiX174 4759 G 1 .$ B F +phiX174 4909 G 1 ^F, K F +phiX174 4910 C 1 , S F +phiX174 4911 T 1 , G F +phiX174 4912 A 1 , R F +phiX174 4913 C 1 , h F +phiX174 4914 A 1 , h F +phiX174 4915 C 1 , W F +phiX174 4916 G 1 , < F +phiX174 4917 C 1 , Q F +phiX174 4918 A 1 , K F +phiX174 4919 G 1 , C F +phiX174 4920 G 1 , = F +phiX174 4921 A 1 , = F +phiX174 4922 C 1 , h F +phiX174 4923 G 1 , h F +phiX174 4924 C 1 , h F +phiX174 4925 T 1 , h F +phiX174 4926 T 1 , h F +phiX174 4927 T 1 , h F +phiX174 4928 T 1 , h F +phiX174 4929 T 1 , P F +phiX174 4930 C 1 , h F +phiX174 4931 A 1 g < F +phiX174 4932 C 1 , h F +phiX174 4933 G 1 , J F +phiX174 4934 T 1 , B F +phiX174 4935 T 1 , h F +phiX174 4936 C 1 , h F +phiX174 4937 T 1 , h F +phiX174 4938 G 1 , h F +phiX174 4939 G 1 , h F +phiX174 4940 T 1 , h F +phiX174 4941 T 1 , h F +phiX174 4942 G 1 , e F +phiX174 4943 G 1 , h F +phiX174 4944 T 1 ,$ h F
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-count.tab Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,1 @@ +10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-coverage.tab Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,4553 @@ +phiX174 392 1 +phiX174 393 1 +phiX174 394 1 +phiX174 395 1 +phiX174 396 1 +phiX174 397 1 +phiX174 398 1 +phiX174 399 1 +phiX174 400 1 +phiX174 401 1 +phiX174 402 1 +phiX174 403 1 +phiX174 404 1 +phiX174 405 1 +phiX174 406 1 +phiX174 407 1 +phiX174 408 1 +phiX174 409 1 +phiX174 410 1 +phiX174 411 1 +phiX174 412 1 +phiX174 413 1 +phiX174 414 1 +phiX174 415 1 +phiX174 416 1 +phiX174 417 1 +phiX174 418 1 +phiX174 419 1 +phiX174 420 1 +phiX174 421 1 +phiX174 422 1 +phiX174 423 1 +phiX174 424 1 +phiX174 425 1 +phiX174 426 1 +phiX174 427 1 +phiX174 428 0 +phiX174 429 0 +phiX174 430 0 +phiX174 431 0 +phiX174 432 0 +phiX174 433 0 +phiX174 434 0 +phiX174 435 0 +phiX174 436 0 +phiX174 437 0 +phiX174 438 0 +phiX174 439 0 +phiX174 440 0 +phiX174 441 0 +phiX174 442 0 +phiX174 443 0 +phiX174 444 0 +phiX174 445 0 +phiX174 446 0 +phiX174 447 0 +phiX174 448 0 +phiX174 449 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4920 1 +phiX174 4921 1 +phiX174 4922 1 +phiX174 4923 1 +phiX174 4924 1 +phiX174 4925 1 +phiX174 4926 1 +phiX174 4927 1 +phiX174 4928 1 +phiX174 4929 1 +phiX174 4930 1 +phiX174 4931 1 +phiX174 4932 1 +phiX174 4933 1 +phiX174 4934 1 +phiX174 4935 1 +phiX174 4936 1 +phiX174 4937 1 +phiX174 4938 1 +phiX174 4939 1 +phiX174 4940 1 +phiX174 4941 1 +phiX174 4942 1 +phiX174 4943 1 +phiX174 4944 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-fasta.fa Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-header.txt Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,3 @@ +@SQ SN:phiX174 LN:5386 +@PG ID:bwa PN:bwa VN:0.5.9-r16 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sam_fa_indices.loc.sample Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a sam_fa_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc +#file has this format (white space characters are TAB characters): +# +#index <seq> <location> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/sam/, +#then the sam_fa_indices.loc entry would look like this: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +# +#and your /depot/data2/galaxy/sam/ directory +#would contain hg18.fa and hg18.fa.fai files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai +# +#Your sam_fa_indices.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of SAMTools indexes and other files --> + <table name="sam_fa_indexes" comment_char="#"> + <columns>line_type, value, path</columns> + <file path="tool-data/sam_fa_indices.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 10 11:55:26 2014 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bamtools" version="2.3.0_2d7685d2ae"> + <repository changeset_revision="9e50b79bc32b" name="package_bamtools" owner="anton" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> \ No newline at end of file