| Next changeset 1:4190f6830fe0 (2018-10-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 |
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added:
macros.xml samtools_bam_to_cram.xml test-data/cached_locally/chr_m.fasta test-data/cached_locally/chr_m.fasta.fai test-data/cached_locally/fasta_indexes.loc test-data/sam_to_bam_out2.bam test-data/test.bam test-data/test.bed test-data/test.cram test-data/test.fa test-data/test.sam test-data/test2.cram tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r b5dc4f88fb2d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 09 11:18:16 2017 -0400 |
| [ |
| @@ -0,0 +1,69 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.3.1">samtools</requirement> + <yield/> + </requirements> + </xml> + <token name="@TOOL_VERSION@">1.3.1</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/},} + </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><![CDATA[samtools 2>&1 | grep Version]]></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 000000000000 -r b5dc4f88fb2d samtools_bam_to_cram.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_bam_to_cram.xml Tue May 09 11:18:16 2017 -0400 |
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| @@ -0,0 +1,137 @@ +<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@"> + <description>convert BAM alignments to CRAM format</description> + + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + + <command><![CDATA[ + #if str( $input_alignment.metadata.bam_index ) != "None": + ln + -f + -s + '${input_alignment.metadata.bam_index}' + '${input_alignment}.bai' + && + #end if + + #if $reference_source.reference_source_selector == 'history': + #set ref_fa = 'ref.fa' + ln -s '${reference_source.input_reference}' ref.fa && + #else: + #set ref_fa = str( $reference_source.input_reference.fields.path ) + #end if + + samtools view + #if $parameter_regions.target_region == "regions_bed_file" + -L '${parameter_regions.regions_bed_file}' + #end if + + -@\${GALAXY_SLOTS:-1} + -C + -T '$ref_fa' + -o '${output_alignment}' + + '${input_alignment}' + + #if $parameter_regions.target_region == "region" + '${parameter_regions.region_string}' + #end if + ]]></command> + + <inputs> + <param name="input_alignment" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="input_reference" type="select" label="Reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input_alignment" key="dbkey" column="1" /> + </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"> + <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/> + </when> + </conditional> + <conditional name="parameter_regions"> + <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)"> + <option value="entire_input_file">Entire BAM alignment file</option> + <option value="region">Specific region</option> + <option value="regions_bed_file">List of specific regions (BED file)</option> + </param> + <when value="entire_input_file" /> + <when value="region"> + <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" /> + </when> + <when value="regions_bed_file"> + <param name="regions_bed_file" argument="-L" type="data" format="bed" + label="Only include reads overlapping this BED file" /> + </when> + </conditional> + </inputs> + + <outputs> + <data name="output_alignment" format="cram" label="$tool.name on ${on_string}.cram"></data> + </outputs> + + <tests> + <test> + <param name="input_alignment" value="test.bam" ftype="bam" /> + <param name="reference_source_selector" value="history" /> + <param name="input_reference" value="test.fa" /> + <param name="target_region" value="entire_input_file" /> + + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + </test> + <test> + <param name="input_alignment" value="test.sam" ftype="sam" /> + <param name="reference_source_selector" value="history" /> + <param name="input_reference" value="test.fa" /> + <param name="target_region" value="entire_input_file" /> + + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + </test> + <test> + <param name="input_alignment" value="test.bam" ftype="bam" /> + <param name="reference_source_selector" value="history" /> + <param name="input_reference" value="test.fa" /> + <param name="target_region" value="region" /> + <param name="region_string" value="CHROMOSOME_I" /> + + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + </test> + <test> + <param name="input_alignment" value="test.bam" ftype="bam" /> + <param name="reference_source_selector" value="history" /> + <param name="input_reference" value="test.fa" /> + <param name="target_region" value="regions_bed_file" /> + <param name="regions_bed_file" value="test.bed" ftype="bed" /> + + <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> + </test> + <test> + <param name="input_alignment" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" /> + <param name="reference_source_selector" value="cached" /> + <param name="input_reference" value="equCab2chrM" /> + <param name="target_region" value="entire_input_file" /> + <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" /> + </test> + </tests> + + <help><![CDATA[ +**What this tool does** + +Converts alignments from the BAM format to the CRAM format using the ``samtools view`` command. +The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient. + ]]></help> + + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r b5dc4f88fb2d 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 May 09 11:18:16 2017 -0400 |
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| 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 000000000000 -r b5dc4f88fb2d 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 May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chrM 16660 6 50 51 |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d 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 May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +equCab2chrM equCab2 Horse (Equus caballus): equCab2 chrM ${__HERE__}/chr_m.fasta |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d test-data/sam_to_bam_out2.bam |
| b |
| Binary file test-data/sam_to_bam_out2.bam has changed |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d test-data/test.bam |
| b |
| Binary file test-data/test.bam has changed |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d test-data/test.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.bed Tue May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +CHROMOSOME_I 1 120 |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d test-data/test.cram |
| b |
| Binary file test-data/test.cram has changed |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d test-data/test.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fa Tue May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>CHROMOSOME_I +gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc +ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d test-data/test.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.sam Tue May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,15 @@ +@HD VN:1.4 SO:unsorted +@SQ SN:CHROMOSOME_I LN:100 +@RG ID:UNKNOWN SM:UNKNOWN +@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5 +@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2 +SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU +SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU +SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA <?@<@A8>0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.3743423 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ##################?6@:7<=@3=@ABAAB>BDBBABADABDDDBDDBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.4251890 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###########@BB=BCBBC?B>B;>B@@ADBBB@DBBBBDCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.5238868 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA @,=@@D8D;?BBB>;?BBB==BB@D;>D>BBB>BBDDB<DABADCACDCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.6023338 0 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAGCTAC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCDDDBCCABB=DABBA?################ RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-6 YT:Z:UU +SRR065390.6815812 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############?@.@?B;B0B=;<DADB@@BDDBBDDBCBCBD@CCDCCCCCCCDCCCCCCCCACCCCCCCCCCBCCCCCCDCCCCCCCCCCCBCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.6905811 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #######################BB@>A<BC>@@BCCB@=BACBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.8289592 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################A?@C9@@BC=AABDD@A@DC@CB=@BA?6@CCAAC@+CCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d test-data/test2.cram |
| b |
| Binary file test-data/test2.cram has changed |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Tue May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,29 @@ +#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 fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.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: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r b5dc4f88fb2d tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue May 09 11:18:16 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/fasta_indexes.loc" /> + </table> +</tables> |