| Previous changeset 5:c73bf16b45df (2015-03-05) Next changeset 7:881e16ad05c6 (2015-11-11) |
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Commit message:
Uploaded |
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modified:
sam_to_bam.xml tool_dependencies.xml |
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added:
macros.xml test-data/cached_locally/all_fasta.loc test-data/cached_locally/chr_m.fasta test-data/cached_locally/chr_m.fasta.fai test-data/cached_locally/fasta_indexes.loc test-data/chr_m.fasta.fai tool_data_table_conf.xml.test |
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removed:
sam_to_bam.py |
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| diff -r c73bf16b45df -r d04d9f1c6791 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 21 14:52:20 2015 -0400 |
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| @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + +</macros> |
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| diff -r c73bf16b45df -r d04d9f1c6791 sam_to_bam.py --- a/sam_to_bam.py Thu Mar 05 21:28:25 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,172 +0,0 @@\n-#!/usr/bin/env python\n-"""\n-Converts SAM data to sorted BAM data.\n-usage: sam_to_bam.py [options]\n- --input1: SAM file to be converted\n- --index: path of the indexed reference genome\n- --ref_file: Reference file if choosing from history\n- --output1: output dataset in bam format\n-"""\n-\n-import optparse, os, sys, subprocess, tempfile, shutil\n-\n-def stop_err( msg ):\n- sys.stderr.write( \'%s\\n\' % msg )\n- sys.exit()\n-\n-def __main__():\n- #Parse Command Line\n- parser = optparse.OptionParser()\n- parser.add_option( \'\', \'--input1\', dest=\'input1\', help=\'The input SAM dataset\' )\n- \n- parser.add_option( \'\', \'--index\', dest=\'index\', help=\'The path of the indexed reference genome\' )\n- parser.add_option( \'\', \'--ref_file\', dest=\'ref_file\', help=\'The reference dataset from the history\' )\n- parser.add_option( \'\', \'--output1\', dest=\'output1\', help=\'The output BAM dataset\' )\n- ( options, args ) = parser.parse_args()\n-\n- # output version # of tool\n- try:\n- tmp = tempfile.NamedTemporaryFile().name\n- tmp_stdout = open( tmp, \'wb\' )\n- proc = subprocess.Popen( args=\'samtools 2>&1\', shell=True, stdout=tmp_stdout )\n- tmp_stdout.close()\n- returncode = proc.wait()\n- stdout = None\n- for line in open( tmp_stdout.name, \'rb\' ):\n- if line.lower().find( \'version\' ) >= 0:\n- stdout = line.strip()\n- break\n- if stdout:\n- sys.stdout.write( \'Samtools %s\\n\' % stdout )\n- else:\n- raise Exception\n- except:\n- sys.stdout.write( \'Could not determine Samtools version\\n\' )\n-\n- tmp_dir = tempfile.mkdtemp( dir=\'.\' )\n- if not options.ref_file or options.ref_file == \'None\':\n- # We\'re using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).\n- # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in\n- # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai\n- fai_index_file_path = \'%s.fai\' % options.index\n- if not os.path.exists( fai_index_file_path ):\n- #clean up temp files\n- if os.path.exists( tmp_dir ):\n- shutil.rmtree( tmp_dir )\n- stop_err( \'Indexed genome %s not present, request it by reporting this error.\' % options.index )\n- else:\n- try:\n- # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will:\n- # - index reference sequence in the FASTA format or extract subsequence from indexed reference sequence\n- # - if no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk\n- # - if regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format\n- # - the input file can be compressed in the RAZF format.\n- # IMPORTANT NOTE: a real weakness here is that we are creating indexes for the history dataset\n- # every time we run this tool. It would be nice if we could somehow keep track of user\'s specific\n- # index files so they could be re-used.\n- fai_index_file_base = tempfile.NamedTemporaryFile( dir=tmp_dir ).name\n- # At this point, fai_index_file_path will look something like /tmp/dataset_13.dat\n- os.symlink( options.ref_file, fai_index_file_base )\n- fai_index_file_path = \'%s.fai\' % fai_index_file_base\n- command = \'samtools faidx %s\' % fai_index_file_base\n- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name\n- tmp_stderr = open( tmp, \'wb\' )\n- proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )\n- returncode = proc.wait()\n- tmp_stderr.close()\n- # get stderr, allowing for case where it\'s very large\n- tmp_stderr = open( tmp, \'rb\' )\n- stderr = \''..b'.close()\n- if returncode != 0:\n- raise Exception, stderr \n- if os.path.getsize( fai_index_file_path ) == 0:\n- raise Exception, \'Index file empty, there may be an error with your reference file or settings.\'\n- except Exception, e:\n- #clean up temp files\n- if os.path.exists( tmp_dir ):\n- shutil.rmtree( tmp_dir )\n- stop_err( \'Error creating indexes from reference (%s), %s\' % ( options.ref_file, str( e ) ) )\n- try:\n- # Extract all alignments from the input SAM file to BAM format ( since no region is specified, all the alignments will be extracted ).\n- tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )\n- tmp_aligns_file_name = tmp_aligns_file.name\n- tmp_aligns_file.close()\n- command = \'samtools view -bt %s -o %s %s\' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 )\n- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name\n- tmp_stderr = open( tmp, \'wb\' )\n- proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )\n- returncode = proc.wait()\n- tmp_stderr.close()\n- # get stderr, allowing for case where it\'s very large\n- tmp_stderr = open( tmp, \'rb\' )\n- stderr = \'\'\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read( buffsize )\n- if not stderr or len( stderr ) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- tmp_stderr.close()\n- if returncode != 0:\n- raise Exception, stderr\n- except Exception, e:\n- #clean up temp files\n- if os.path.exists( tmp_dir ):\n- shutil.rmtree( tmp_dir )\n- stop_err( \'Error extracting alignments from (%s), %s\' % ( options.input1, str( e ) ) )\n- try:\n- # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command\n- # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted\n- # into memory ( controlled by option -m ).\n- tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )\n- tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name\n- tmp_sorted_aligns_file.close()\n- command = \'samtools sort %s %s\' % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name )\n- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name\n- tmp_stderr = open( tmp, \'wb\' )\n- proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )\n- returncode = proc.wait()\n- tmp_stderr.close()\n- # get stderr, allowing for case where it\'s very large\n- tmp_stderr = open( tmp, \'rb\' )\n- stderr = \'\'\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read( buffsize )\n- if not stderr or len( stderr ) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- tmp_stderr.close()\n- if returncode != 0:\n- raise Exception, stderr\n- except Exception, e:\n- #clean up temp files\n- if os.path.exists( tmp_dir ):\n- shutil.rmtree( tmp_dir )\n- stop_err( \'Error sorting alignments from (%s), %s\' % ( tmp_aligns_file_name, str( e ) ) )\n- # Move tmp_aligns_file_name to our output dataset location\n- sorted_bam_file = \'%s.bam\' % tmp_sorted_aligns_file_name\n- shutil.move( sorted_bam_file, options.output1 )\n- #clean up temp files\n- if os.path.exists( tmp_dir ):\n- shutil.rmtree( tmp_dir )\n- # check that there are results in the output file\n- if os.path.getsize( options.output1 ) > 0:\n- sys.stdout.write( \'SAM file converted to BAM\' )\n- else:\n- stop_err( \'Error creating sorted version of BAM file.\' )\n-\n-if __name__=="__main__": __main__()\n' |
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| diff -r c73bf16b45df -r d04d9f1c6791 sam_to_bam.xml --- a/sam_to_bam.xml Thu Mar 05 21:28:25 2015 -0500 +++ b/sam_to_bam.xml Tue Apr 21 14:52:20 2015 -0400 |
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| b'@@ -1,99 +1,84 @@\n-<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.4">\n- <description>converts SAM format to BAM format</description>\n- <requirements>\n- <requirement type="package" version="0.1.19">samtools</requirement>\n- </requirements>\n- <command interpreter="python">\n- sam_to_bam.py\n- --input1=$source.input1\n- #if $source.index_source == "history":\n- --ref_file=$source.ref_file\n- #else\n- --index=${source.index.fields.path}\n- #end if\n- --output1=$output1\n- </command>\n- <inputs>\n- <conditional name="source">\n- <param name="index_source" type="select" label="Choose the source for the reference list">\n- <option value="cached">Locally cached</option>\n- <option value="history">History</option>\n- </param>\n- <when value="cached">\n- <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert">\n- <validator type="unspecified_build" />\n- <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />\n- </param>\n- <param name="index" type="select" label="Using reference genome">\n- <options from_data_table="fasta_indexes">\n- <filter type="data_meta" ref="input1" key="dbkey" column="1" />\n- <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />\n- </options>\n- </param>\n- </when>\n- <when value="history">\n- <param name="input1" type="data" format="sam" label="SAM file to convert" />\n- <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />\n- </when>\n- </conditional>\n- </inputs>\n- <outputs>\n- <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">\n- <actions>\n- <conditional name="source.index_source">\n- <when value="cached">\n- <action type="metadata" name="dbkey">\n- <option type="from_param" name="source.input1" param_attribute="dbkey" />\n- </action>\n- </when>\n- <when value="history">\n- <action type="metadata" name="dbkey">\n- <option type="from_param" name="source.ref_file" param_attribute="dbkey" />\n- </action>\n- </when>\n+<tool id="sam_to_bam" name="SAM-to-BAM" version="2.0">\n+ <description>convert SAM to BAM</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"></expand>\n+ <expand macro="version_command"></expand>\n+ <expand macro="stdio"></expand>\n+ <command>\n+ <![CDATA[\n+ samtools sort -O bam -@ \\${GALAXY_SLOTS:-1} -o sorted_input.bam -T temp "$input1" && \n+ #if $source.index_source == "history":\n+ ln -s $source.ref_file input.fa &&\n+ samtools faidx input.fa &&\n+ #else\n+ ln -s ${source.index.fields.path} input.fa &&\n+ ln -s ${source.index.fields.path}.fai input.fa.fai &&\n+ #end if\n+ samtools view -@ \\${GALAXY_SLOTS:-1} -b -h -o $output1 -T input.fa sorted_input.bam\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="source">\n+ <param label="Choose the source for the reference genome" name="index_source" type="select">\n+ <option value="cached">Use a built-in genome</option>\n+ <option value="history">Use a genome from the history</option>\n+ </param>\n+ <when value="cached">\n+ <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data">\n+ <validator type="unspecified_build" />\n+ <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="db'..b' table_name="fasta_indexes" type="dataset_metadata_in_data_table" />\n+ </param>\n+ <param label="Using reference genome" name="index" type="select">\n+ <options from_data_table="fasta_indexes">\n+ <filter column="1" key="dbkey" ref="input1" type="data_meta" />\n+ <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param format="sam" label="SAM file to convert" name="input1" type="data" />\n+ <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" />\n+ </when>\n </conditional>\n- </actions>\n- </data>\n- </outputs>\n- <tests>\n- <test>\n- <!--\n- Sam-to-Bam command:\n- cp test-data/chr_m.fasta .\n- samtools faidx chr_m.fasta\n- samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam\n- samtools sort unsorted.bam sam_to_bam_out1\n- chr_m.fasta is the reference file (chrM from equCab2)\n- -->\n- <param name="index_source" value="history" /> \n- <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />\n- <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />\n- <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />\n- </test>\n- <test>\n- <!--\n- Sam-to-Bam command:\n- samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam\n- samtools sort unsorted.bam sam_to_bam_out2\n- chr_m.fasta is the reference file and the index chr_m.fasta.fai \n- these should be in the same directory, and chrM is from equCab2\n- -->\n- <param name="index_source" value="cached" />\n- <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />\n- <param name="index" value="chr_m" />\n- <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />\n- </test>\n- </tests>\n- <help>\n-\n+ </inputs>\n+ <outputs>\n+ <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1">\n+ <actions>\n+ <conditional name="source.index_source">\n+ <when value="cached">\n+ <action name="dbkey" type="metadata">\n+ <option name="source.input1" param_attribute="dbkey" type="from_param" />\n+ </action>\n+ </when>\n+ <when value="history">\n+ <action name="dbkey" type="metadata">\n+ <option name="source.ref_file" param_attribute="dbkey" type="from_param" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="index_source" value="history" />\n+ <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />\n+ <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />\n+ <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n **What it does**\n \n-This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.\n+Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands::\n \n-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml\n+ samtools sort -O bam -o sorted_input.bam [INPUT SAM] \n+ samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam\n \n+]]>\n </help>\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btp352</citation>\n- </citations>\n+ <expand macro="citations"></expand>\n </tool>\n' |
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| diff -r c73bf16b45df -r d04d9f1c6791 test-data/cached_locally/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/all_fasta.loc Tue Apr 21 14:52:20 2015 -0400 |
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| @@ -0,0 +1,1 @@ +chrM chr_m Horse (Equus caballus): equCab2 chrM ${__HERE__}/chrM.fasta |
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| diff -r c73bf16b45df -r d04d9f1c6791 test-data/cached_locally/chr_m.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/chr_m.fasta Tue Apr 21 14:52:20 2015 -0400 |
| b |
| b'@@ -0,0 +1,335 @@\n+>chrM\n+GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA\n+GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT\n+TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT\n+CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA\n+AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG\n+ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG\n+GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA\n+ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA\n+AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA\n+AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA\n+TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA\n+AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT\n+GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC\n+CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT\n+CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA\n+AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT\n+TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC\n+TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT\n+GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT\n+CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA\n+CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG\n+TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA\n+TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC\n+TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG\n+AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG\n+ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT\n+AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC\n+CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT\n+ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG\n+AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA\n+ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA\n+AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA\n+ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG\n+TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA\n+ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG\n+TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA\n+CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA\n+TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA\n+AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT\n+ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC\n+AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca\n+taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt\n+tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg\n+cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG\n+ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT\n+TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC\n+CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA\n+TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG\n+CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG\n+TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT\n+CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT\n+CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT\n+AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA\n+AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg\n+tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt\n+caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT\n+GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT\n+CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG\n+GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA\n+CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT\n+AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC\n+CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC\n+CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA\n+CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG\n+TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC\n+ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC\n+ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA\n+ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA\n+TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA\n+ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG\n+GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC\n+ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA\n+CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC\n+TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA\n+CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT\n+ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact\n+acaggaattgaacctgctcct'..b'CATTATCCACAGCCTAAATGACGAGCAAGATATC\n+CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT\n+AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT\n+ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC\n+TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG\n+TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC\n+TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC\n+CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA\n+CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG\n+CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG\n+ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC\n+CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG\n+CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC\n+TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC\n+CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT\n+CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG\n+TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA\n+ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC\n+CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA\n+CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT\n+AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC\n+AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG\n+TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC\n+ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC\n+CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG\n+AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA\n+ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT\n+GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC\n+GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA\n+CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG\n+AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT\n+ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA\n+GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC\n+AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG\n+GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC\n+ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT\n+ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT\n+ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC\n+AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT\n+CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT\n+CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC\n+CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT\n+CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA\n+ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA\n+TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT\n+AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC\n+CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC\n+CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT\n+CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT\n+CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC\n+ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT\n+ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC\n+TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC\n+TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT\n+CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC\n+CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG\n+TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA\n+GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC\n+AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC\n+GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG\n+CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT\n+TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA\n+ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA\n+CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT\n+CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA\n+CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA\n+GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac\n+ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct\n+gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt\n+gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc\n+acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac\n+ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA\n+CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT\n+GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT\n+AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA\n+GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT\n+TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC\n+TTCTTCCCCC\n' |
| b |
| diff -r c73bf16b45df -r d04d9f1c6791 test-data/cached_locally/chr_m.fasta.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/chr_m.fasta.fai Tue Apr 21 14:52:20 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chrM 16660 6 50 51 |
| b |
| diff -r c73bf16b45df -r d04d9f1c6791 test-data/cached_locally/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/fasta_indexes.loc Tue Apr 21 14:52:20 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chrM chr_m Horse (Equus caballus): equCab2 chrM ${__HERE__}/chrM.fasta |
| b |
| diff -r c73bf16b45df -r d04d9f1c6791 test-data/chr_m.fasta.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr_m.fasta.fai Tue Apr 21 14:52:20 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chrM 16660 6 50 51 |
| b |
| diff -r c73bf16b45df -r d04d9f1c6791 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Apr 21 14:52:20 2015 -0400 |
| b |
| @@ -0,0 +1,10 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/fasta_indexes.loc" /> + </table> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r c73bf16b45df -r d04d9f1c6791 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 05 21:28:25 2015 -0500 +++ b/tool_dependencies.xml Tue Apr 21 14:52:20 2015 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="samtools" version="1.2"> + <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |