| Next changeset 1:2ec7f09c813f (2014-09-10) |
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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 |
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| diff -r 000000000000 -r 2c2200cecea2 bamtools-filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools-filter.xml Wed Sep 10 11:55:26 2014 -0400 |
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| b'@@ -0,0 +1,328 @@\n+<tool id="bamFilter" name="Filter" version="0.0.1">\r\n+ <description>BAM datasets on a variety of attributes</description>\r\n+ <requirements>\r\n+ <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>\r\n+ </requirements>\r\n+ <command>\r\n+\r\n+ cat $script_file > $out_file2;\r\n+ \r\n+ #for $bam_count, $input_bam in enumerate( $input_bams ):\r\n+ ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&\r\n+ ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\r\n+ #end for\r\n+ \r\n+ bamtools\r\n+ filter\r\n+ -script $script_file\r\n+ \r\n+ #for $bam_count, $input_bam in enumerate( $input_bams ):\r\n+ -in "localbam_${bam_count}.bam"\r\n+ #end for\r\n+ -out $out_file1\r\n+ \r\n+ </command>\r\n+\r\n+ <inputs>\r\n+ <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">\r\n+ <param name="input_bam" type="data" format="bam" label="BAM dataset" />\r\n+ </repeat>\r\n+ <repeat name="conditions" title="Condition" min="1">\r\n+ <repeat name="filters" title="Filter" min="1">\r\n+ <conditional name="bam_property">\r\n+ <param name="bam_property_selector" type="select" label="Select BAM property to filter on">\r\n+ <option value="alignmentFlag"/>\r\n+ <option value="cigar"/>\r\n+ <option value="insertSize"/>\r\n+ <option value="isDuplicate"/>\r\n+ <option value="isFailedQC"/>\r\n+ <option value="isFirstMate"/>\r\n+ <option value="isMapped"/>\r\n+ <option value="isMateMapped"/>\r\n+ <option value="isMateReverseStrand"/>\r\n+ <option value="isPaired"/>\r\n+ <option value="isPrimaryAlignment"/>\r\n+ <option value="isProperPair"/>\r\n+ <option value="isReverseStrand"/>\r\n+ <option value="isSecondMate"/>\r\n+ <option selected="True" value="mapQuality"/>\r\n+ <option value="matePosition"/>\r\n+ <option value="mateReference"/>\r\n+ <option value="name"/>\r\n+ <option value="position"/>\r\n+ <option value="queryBases"/>\r\n+ <option value="reference"/>\r\n+ <option value="tag"/>\r\n+ </param>\r\n+ <!-- would be fanstastic to have AND and OR constructs in when statements -->\r\n+ <when value="alignmentFlag">\r\n+ <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"/>\r\n+ </when>\r\n+ <when value="cigar">\r\n+ <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"/>\r\n+ </when>\r\n+ <when value="insertSize">\r\n+ <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"">\r\n+ <sanitizer invalid_char="">\r\n+ <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>\r\n+ </sanitizer>\r\n+ </param>\r\n+ </when>\r\n+ <when value="isDuplicate">\r\n+ <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" />\r\n+ </when>\r\n+ <when value="isFailedQC">\r\n+ <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/>\r\n+ </when>\r\n+ <when value="isFirstMate">\r\n+ <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="f'..b'AM dataset(s) to filter**\r\n+\r\n+*Conditions and Filters*\r\n+\r\n+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.\r\n+\r\n+-----\r\n+\r\n+**Example 1. Using a single filter**\r\n+\r\n+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).\r\n+For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:\r\n+\r\n+.. image:: ${static_path}/images/simple-filter.png\r\n+\r\n+-----\r\n+\r\n+**Example 2. Using multiple filters**\r\n+\r\n+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.\r\n+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):\r\n+\r\n+.. image:: ${static_path}/images/multiple-filters.png\r\n+\r\n+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.\r\n+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.\r\n+\r\n+-----\r\n+\r\n+**Example 3. Complex filtering with multiple conditions**\r\n+\r\n+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*) \r\n+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*. \r\n+The following screenshot expalins how this can be done:\r\n+\r\n+.. image:: ${static_path}/images/complex-filters.png\r\n+\r\n+-----\r\n+\r\n+**Example 4. Even more complex filtering with Rules**\r\n+\r\n+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.\r\n+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\r\n+filtering will look like this::\r\n+\r\n+ !(1) & (2 | 3)\r\n+ \r\n+Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:\r\n+\r\n+.. image:: ${static_path}/images/rule.png\r\n+\r\n+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.\r\n+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::\r\n+\r\n+ NOT condition 1 AND (condition 2 OR condition 3)\r\n+\r\n+-----\r\n+\r\n+**JSON script file**\r\n+\r\n+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.\r\n+For instance, the example 4 looks like this in the JSON form::\r\n+\r\n+ {\r\n+ "filters":\r\n+ [\r\n+ { "id": "1",\r\n+ "tag":"NM:=0",\r\n+ "isReverseStrand":"false"\r\n+ },\r\n+ { "id": "2",\r\n+ "tag":"NM:>0",\r\n+ "isReverseStrand":"true"\r\n+ }\r\n+ ]\r\n+ }\r\n+ \r\n+ \r\n+\r\n+-----\r\n+\r\n+**More information**\r\n+\r\n+.. class:: infomark\r\n+\r\n+Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki\r\n+\r\n+\r\n+</help>\r\n+</tool>\r\n' |
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| diff -r 000000000000 -r 2c2200cecea2 bamtools-split.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools-split.xml Wed Sep 10 11:55:26 2014 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r 2c2200cecea2 bamtools.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools.xml Wed Sep 10 11:55:26 2014 -0400 |
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| b'@@ -0,0 +1,290 @@\n+<?xml version="1.0"?>\n+<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1">\n+ <description>BAM datasets and perform other transformations</description>\n+ <requirements>\n+ <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>\n+ <requirement type="package" version="0.1.18">samtools</requirement>\n+ </requirements>\n+ \n+ <command>\n+ ##set up input files\n+ \n+ #for $bam_count, $input_bam in enumerate( $input_bams ):\n+ ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&\n+ ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\n+ #end for\n+ \n+ #if str( $analysis_type.analysis_type_selector ) == "convert":\n+ #if str( $analysis_type.format_type.format_type_selector ) == "pileup":\n+ #set $reference_fasta_filename = "localref.fa"\n+ #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":\n+ ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&\n+ samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&\n+ #else:\n+ #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )\n+ #end if\n+ #end if\n+ #end if\n+\n+ ##finished setting up inputs\n+ \n+ ##start bamtools commandline\n+ \n+ bamtools\n+ \n+ #if str( $analysis_type.analysis_type_selector ) == "convert":\n+ \n+ convert\n+ \n+ -format ${analysis_type.format_type.format_type_selector}\n+ \n+ #if str( $analysis_type.format_type.format_type_selector ) == "pileup":\n+ \n+ ${analysis_type.format_type.mapqual}\n+ -fasta "${reference_fasta_filename}"\n+ \n+ #elif str( $analysis_type.format_type.format_type_selector ) == "sam":\n+ \n+ ${analysis_type.format_type.noheader}\n+ \n+ #end if\n+ \n+ -out $out_file1\n+ \n+ #elif str( $analysis_type.analysis_type_selector ) == "count":\n+ \n+ count\n+ > $out_file1\n+ \n+ #elif str( $analysis_type.analysis_type_selector ) == "coverage":\n+ \n+ coverage\n+ -out $out_file1\n+ \n+ #elif str( $analysis_type.analysis_type_selector ) == "header":\n+ \n+ header\n+ > $out_file1\n+ \n+ #elif str( $analysis_type.analysis_type_selector ) == "merge":\n+ \n+ merge\n+ -out $out_file1\n+ \n+ #elif str( $analysis_type.analysis_type_selector ) == "random":\n+ \n+ random\n+ -n ${analysis_type.count}\n+ -seed ${analysis_type.seed}\n+ -out $out_file1\n+ \n+ #elif str( $analysis_type.analysis_type_selector ) == "revert":\n+ \n+ revert\n+ ${analysis_type.keepDuplicate}\n+ ${analysis_type.keepQualities}\n+ -out $out_file1\n+ \n+ #elif str( $analysis_type.analysis_type_selector ) == "sort":\n+ \n+ sort\n+ ${analysis_type.byname}\n+ -out $out_file1\n+ \n+ #end if\n+ \n+ #for $bam_count, $input_bam in enumerate( $input_bams ):\n+ -in "localbam_${bam_count}.bam"\n+ #end for\n+ \n+ \n+ </command>\n+ <inputs>\n+ \n+ <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">\n+ <param name="input_bam" type="data" format="bam" label="BAM dataset" />\n+ </repeat>\n+\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">\n+ <option value="convert">Convert</option>\n+ <option value="count">Count</option>\n+ <option value="coverage">Coverage</option>\n+ <option value="header">Header</option>\n+ <option value="merge">Merge</option>\n+ <option value="random">Random</option>\n+ <option value="revert">Revert</option>\n+ <!-- The sort option below is commented out as BAM files in Galaxy as reference sorted by dafault. -->\n+ <!-- Allowing u'..b'evalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>\n+ </when>\n+ </conditional>\n+ \n+ </inputs>\n+ <outputs>\n+ <data format="txt" name="out_file1">\n+ <change_format>\n+ <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />\n+ <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />\n+ <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />\n+ <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />\n+ <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />\n+ <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />\n+ <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />\n+ <when input="analysis_type.analysis_type_selector" value="random" format="bam" />\n+ <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />\n+ <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />\n+ </change_format>\n+ </data> \n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>\n+ <param name="analysis_type_selector" value="convert"/>\n+ <param name="format_type_selector" value="pileup"/>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="mapqual" value="true" />\n+ <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>\n+ <output name="output_bam" file="bamtools-convert-pileup.pu" />\n+ </test>\n+ <test>\n+ <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>\n+ <param name="analysis_type_selector" value="count"/>\n+ <output name="output_bam" file="bamtools-count.tab" />\n+ </test>\n+ <test>\n+ <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>\n+ <param name="analysis_type_selector" value="coverage"/>\n+ <output name="output_bam" file="bamtools-coverage.tab" />\n+ </test>\n+ <test>\n+ <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>\n+ <param name="analysis_type_selector" value="header"/>\n+ <output name="output_bam" file="bamtools-header.txt" />\n+ </test>\n+ </tests>\n+ \n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ \n+ <help>\n+\n+**What is does**\n+\n+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).\n+This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.\n+\n+-----\n+\n+**Convert**\n+\n+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\n+cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.\n+\n+-----\n+\n+**Count**\n+\n+Counts a number of alignments in a BAM dataset(s).\n+\n+-----\n+\n+**Coverage**\n+\n+Prints per-base coverage for a BAM dataset.\n+\n+-----\n+\n+**Header**\n+\n+Prints header from a BAM dataset(s).\n+\n+------\n+\n+**Merge**\n+\n+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.\n+\n+------\n+\n+**Random**\n+\n+Grabs a specified number of random lines from BAM dataset(s).\n+\n+------\n+\n+**Revert**\n+\n+Removes duplicate marks and restores original (non-recalibrated) base qualities.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**More information**\n+\n+Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-convert-pileup.pu --- /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 |
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| @@ -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 |
| b |
| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-count.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-count.tab Wed Sep 10 11:55:26 2014 -0400 |
| b |
| @@ -0,0 +1,1 @@ +10 |
| b |
| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-coverage.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-coverage.tab Wed Sep 10 11:55:26 2014 -0400 |
| b |
| b'@@ -0,0 +1,4553 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|
| b |
| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-fasta.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-fasta.fa Wed Sep 10 11:55:26 2014 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA |
| b |
| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-header.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools-header.txt Wed Sep 10 11:55:26 2014 -0400 |
| b |
| @@ -0,0 +1,3 @@ +@SQ SN:phiX174 LN:5386 +@PG ID:bwa PN:bwa VN:0.5.9-r16 + |
| b |
| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-input1.bam |
| b |
| Binary file test-data/bamtools-input1.bam has changed |
| b |
| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-split-test1.bam |
| b |
| Binary file test-data/bamtools-split-test1.bam has changed |
| b |
| diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-test1.bam |
| b |
| Binary file test-data/bamtools-test1.bam has changed |
| b |
| diff -r 000000000000 -r 2c2200cecea2 tool-data/sam_fa_indices.loc.sample --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 2c2200cecea2 tool-data/tool_data_table_conf.xml.sample --- /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 |
| b |
| @@ -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> |
| b |
| diff -r 000000000000 -r 2c2200cecea2 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 10 11:55:26 2014 -0400 |
| b |
| @@ -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 |
