# HG changeset patch
# User anton
# Date 1410364526 14400
# Node ID 2c2200cecea26083c3bc2be7f7c900ad0e4d7d9b
Uploaded
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
@@ -0,0 +1,328 @@
+
+ BAM datasets on a variety of attributes
+
+ bamtools
+
+
+
+ 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
+
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+ ##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
+
+
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+
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+
+
+
+
+
+
+**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
+
+
+
+
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
@@ -0,0 +1,116 @@
+
+ BAM datasets on variety of attributes
+
+ bamtools
+
+
+
+ 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
+
+
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+
+**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
+
+
+
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
@@ -0,0 +1,290 @@
+
+
+ BAM datasets and perform other transformations
+
+ bamtools
+ samtools
+
+
+
+ ##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
+
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+**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
+
+
+
diff -r 000000000000 -r 2c2200cecea2 images/complex-filters.png
Binary file images/complex-filters.png has changed
diff -r 000000000000 -r 2c2200cecea2 images/multiple-filters.png
Binary file images/multiple-filters.png has changed
diff -r 000000000000 -r 2c2200cecea2 images/rule.png
Binary file images/rule.png has changed
diff -r 000000000000 -r 2c2200cecea2 images/single-filter.png
Binary file images/single-filter.png has changed
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
@@ -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
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+phiX174 400 T 1 , H F
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+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
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+phiX174 427 C 1 , h F
+phiX174 428 C 1 ,$ h F
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+phiX174 1365 A 1 , G :
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+phiX174 1374 T 1 , = :
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+phiX174 2470 G 1 . h :
+phiX174 2471 C 1 A ? :
+phiX174 2472 T 1 . U :
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+phiX174 2476 T 1 . b :
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+phiX174 2478 G 1 . h :
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+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 . = :
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+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 .$. hh :F
+phiX174 4269 G 1 . [ F
+phiX174 4270 A 1 . H F
+phiX174 4271 A 1 . N F
+phiX174 4272 T 1 . h F
+phiX174 4273 T 1 . h F
+phiX174 4274 G 1 . h F
+phiX174 4275 G 1 . h F
+phiX174 4276 C 1 . h F
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+phiX174 4278 C 1 . h F
+phiX174 4279 A 1 . ? F
+phiX174 4280 A 1 . N F
+phiX174 4281 T 1 . I F
+phiX174 4282 G 1 . c F
+phiX174 4283 C 1 . h F
+phiX174 4284 T 1 . F F
+phiX174 4285 A 1 . ] F
+phiX174 4286 C 1 . h F
+phiX174 4287 A 1 . g F
+phiX174 4288 A 1 . X F
+phiX174 4289 T 1 G > F
+phiX174 4290 G 1 . V F
+phiX174 4291 T 1 .$ 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
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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
@@ -0,0 +1,1 @@
+10
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
@@ -0,0 +1,4553 @@
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+phiX174 4877 0
+phiX174 4878 0
+phiX174 4879 0
+phiX174 4880 0
+phiX174 4881 0
+phiX174 4882 0
+phiX174 4883 0
+phiX174 4884 0
+phiX174 4885 0
+phiX174 4886 0
+phiX174 4887 0
+phiX174 4888 0
+phiX174 4889 0
+phiX174 4890 0
+phiX174 4891 0
+phiX174 4892 0
+phiX174 4893 0
+phiX174 4894 0
+phiX174 4895 0
+phiX174 4896 0
+phiX174 4897 0
+phiX174 4898 0
+phiX174 4899 0
+phiX174 4900 0
+phiX174 4901 0
+phiX174 4902 0
+phiX174 4903 0
+phiX174 4904 0
+phiX174 4905 0
+phiX174 4906 0
+phiX174 4907 0
+phiX174 4908 1
+phiX174 4909 1
+phiX174 4910 1
+phiX174 4911 1
+phiX174 4912 1
+phiX174 4913 1
+phiX174 4914 1
+phiX174 4915 1
+phiX174 4916 1
+phiX174 4917 1
+phiX174 4918 1
+phiX174 4919 1
+phiX174 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
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
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
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
@@ -0,0 +1,3 @@
+@SQ SN:phiX174 LN:5386
+@PG ID:bwa PN:bwa VN:0.5.9-r16
+
diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-input1.bam
Binary file test-data/bamtools-input1.bam has changed
diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-split-test1.bam
Binary file test-data/bamtools-split-test1.bam has changed
diff -r 000000000000 -r 2c2200cecea2 test-data/bamtools-test1.bam
Binary file test-data/bamtools-test1.bam has changed
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
@@ -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
+#
+#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
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
@@ -0,0 +1,8 @@
+
+
+
+
+ line_type, value, path
+
+
+
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
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
+
\ No newline at end of file