Repository 'picard'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/picard

Changeset 23:1cd1cf786389 (2019-05-16)
Previous changeset 22:f6ced08779c4 (2019-03-29) Next changeset 24:b9fbec5ac6b2 (2019-05-31)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
added:
picard_CollectSequencingArtifactsMetrics.xml
test-data/cached_locally/picard_BedToIntervalList_ref.fa
test-data/cached_locally/picard_indexes.loc
test-data/err_summary
test-data/pos_details
test-data/pos_summary
test-data/pre_details
test-data/pre_summary
tool_data_table_conf.xml.test
b
diff -r f6ced08779c4 -r 1cd1cf786389 picard_CollectSequencingArtifactsMetrics.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_CollectSequencingArtifactsMetrics.xml Thu May 16 07:13:32 2019 -0400
[
b'@@ -0,0 +1,148 @@\n+<tool id=\'picard_artifact_metrics\' name=\'Picard Collect Sequencing Artifact Metrics\' version="@TOOL_VERSION@.@WRAPPER_VERSION@">\n+  <description>Collect metrics to quantify single-base sequencing artifacts</description>\n+  <macros>\n+    <import>picard_macros.xml</import>\n+    <token name="@WRAPPER_VERSION@">1</token>\n+  </macros>\n+  <expand macro="requirements">\n+    <requirement type="package" version="3.4.1">r-base</requirement>\n+  </expand>\n+  <command detect_errors="exit_code"><![CDATA[\n+    @java_options@\n+    @symlink_element_identifier@\n+    \n+    #set $reference_fasta_filename = "localref.fa"\n+    @handle_reference_source@\n+    \n+    picard \n+    CollectSequencingArtifactMetrics \n+    I=\'$escaped_element_identifier\'\n+    O=\'OutPut\'\n+    R=\'${reference_fasta_filename}\'\n+    AS=${assume_sorted}\n+    CONTEXT_SIZE=${context_size}\n+    INCLUDE_DUPLICATES=\'${duplicates}\'\n+    #if $contexts_to_print \n+      #for $context in str($contexts_to_print).split(\',\'):\n+          CONTEXTS_TO_PRINT=\'${context}\'\n+      #end for;\n+    #end if;\n+    MINIMUM_QUALITY_SCORE=\'${min_quality_score}\'\n+    INCLUDE_UNPAIRED=\'${unpaired}\'\n+    MAXIMUM_INSERT_SIZE=\'${max_size}\'\n+    MINIMUM_INSERT_SIZE=\'${min_size}\'\n+    MINIMUM_MAPPING_QUALITY=\'${minim_map_quality}\';\n+  ]]></command>  \n+  <inputs>\n+    <param name=\'inputFile\' format="sam,bam" type=\'data\' label=\'SAM/BAM Input file\'/>\n+    <conditional name="reference_source">\n+      <param name="reference_source_selector" type="select" label="Load reference genome from">\n+        <option value="cached">Local cache</option>\n+        <option value="history">History</option>\n+      </param>\n+      <when value="cached">\n+        <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">\n+          <options from_data_table="picard_indexes">\n+            <filter type="sort_by" column="2" />\n+            <validator type="no_options" message="No indexes are available" />\n+          </options>\n+          <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>\n+        </param>\n+      </when>\n+      <when value="history">\n+        <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />\n+      </when>\n+    </conditional>\n+  \n+    <param name=\'context_size\' value="1" type=\'integer\' label=\'How many nucleotides (context) on each side to consider\' help=\'e.g NXN corresponds to 1 "N" on each side of "X"\'/>\n+    <param name="contexts_to_print" type="text" label="Contexts to print in the detailed tables, separated by comma (avoid spaces)" help="e.g. (for context size=1) AAA,AGG. Default prints all contexts">\n+        <sanitizer>\n+            <valid initial="string.letters"><add value="," /></valid>\n+        </sanitizer>\n+    </param>  \n+    <param name=\'min_quality_score\' type=\'integer\' value=\'30\' label=\'Minimum base quality score\'/>\n+    <param name="max_size" type="integer" value="600" label="Maximum insert size"/>\n+    <param name="min_size" type="integer" value="30" label="Minimum insert size"/>\n+    <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>\n+    <param name=\'assume_sorted\' type=\'boolean\' label=\'Assume SAM/BAM is sorted\'/>\n+    <param name=\'duplicates\' type=\'boolean\' label=\'Include duplicates\' checked="false" truevalue="true" falsevalue="false"/>\n+    <param name=\'unpaired\' type=\'boolean\' label=\'Include unpaired reads\' checked="false" truevalue="true" falsevalue="false"/>\n+\n+    <expand macro="VS" />\n+\n+  </inputs>\n+\n+  <outputs>\n+    <data name=\'pre_details\' format="tabular"  from_work_dir="OutPut.pre_adapter_detail_metrics" label=\'Detailed table for artifacts introduced prior to the addition of adapters\'/>\n+    <data na'..b' for artifacts introduced posterior to the addition of adapters\'/>\n+    <data name=\'pos_summary\' format="tabular"  from_work_dir="OutPut.bait_bias_summary_metrics" label=\'Summary table for artifacts introduced posterior to the addition of adapters\'/>\n+    <data name=\'err_summary\' format="tabular"  from_work_dir="OutPut.error_summary_metrics" label=\'General Summary of artifactual errors\'/>\n+  </outputs>\n+  \n+  <tests>\n+    <test>\n+      <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" />\n+      <param name="reference_source_selector" value="history"/>\n+      <param name="ref_file" value="picard_BedToIntervalList_ref.fa" />\n+      <param name="context_size" value="1" />\n+      <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />\n+      <output name=\'pre_details\' file=\'pre_details\' ftype="tabular"  value="pre_detail" lines_diff="4"/>\n+      <output name=\'pre_summary\' file=\'pre_summary\' ftype="tabular"  value="pre_summary" lines_diff="4"/>\n+      <output name=\'pos_details\' file=\'pos_details\' ftype="tabular"  value="pos_detail" lines_diff="4"/>\n+      <output name=\'pos_summary\' file=\'pos_summary\' ftype="tabular"  value="pos_summary" lines_diff="4"/>\n+      <output name=\'err_summary\' file=\'err_summary\' ftype="tabular"  value="err_summary" lines_diff="4"/>\n+    </test>\n+    <test>\n+      <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>\n+      <param name="reference_source_selector" value="cached"/>\n+      <param name="context_size" value="1" />\n+      <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />\n+      <output name=\'pre_details\' file=\'pre_details\' ftype="tabular"  value="pre_detail" lines_diff="4"/>\n+      <output name=\'pre_summary\' file=\'pre_summary\' ftype="tabular"  value="pre_summary" lines_diff="4"/>\n+      <output name=\'pos_details\' file=\'pos_details\' ftype="tabular"  value="pos_detail" lines_diff="4"/>\n+      <output name=\'pos_summary\' file=\'pos_summary\' ftype="tabular"  value="pos_summary" lines_diff="4"/>\n+      <output name=\'err_summary\' file=\'err_summary\' ftype="tabular"  value="err_summary" lines_diff="4"/>\n+    </test>\n+  </tests>\n+  <help>\n+\n+.. class:: infomark\n+\n+**Purpose**\n+\n+Program to chart the distribution of potential sequencing "single nucleotide mutation" artifacts in a SAM or BAM file.\n+\n+@dataset_collections@\n+\n+@description@\n+\n+  ASSUME_SORTED=Boolean           If true (default), then the sort order in the header file will be ignored.  \n+                                  Default: True\n+\n+  CONTEXT_SIZE=integer            The number of context bases to include on each side of the assayed base.\n+  \n+  CONTEXT_SIZE_TO_PRINT=String    If specified, only print results for these contexts in the detail metrics output. \n+                                  However, the summary metrics output will still take all contexts into consideration.\n+                                \n+  DB_SNP=text file                VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.\n+\n+  INCLUDE_DUPLICATES=Boolean      Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.\n+\n+  INCLUDE_UNPAIRED=Boolean        Include unpaired reads. If set to true then all paired reads will be included as well - \n+                                  MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.\n+\n+  MAXIMUM_INSERT_SIZE=Integer     The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.\n+                                  Default = 600\n+\n+  MINIMUM_INSERT_SIZE=Integer     The minimum insert size for a read to be included in analysis. Default = 60\n+\n+  MINIMUM_MAPPING_QUALITY         The minimum mapping quality score for a base to be included in analysis. Default = 30\n+\n+  MINIMUM_QUALITY_SCORE           The minimum base quality score for a base to be included in analysis. Default = 20\n+\n+@more_info@\n+\n+  </help>\n+  <expand macro="citations" />\n+</tool>\n'
b
diff -r f6ced08779c4 -r 1cd1cf786389 test-data/cached_locally/picard_BedToIntervalList_ref.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/picard_BedToIntervalList_ref.fa Thu May 16 07:13:32 2019 -0400
b
b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n'
b
diff -r f6ced08779c4 -r 1cd1cf786389 test-data/cached_locally/picard_indexes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/picard_indexes.loc Thu May 16 07:13:32 2019 -0400
b
@@ -0,0 +1,2 @@
+chrM chrM ChrM ${__HERE__}/picard_BedToIntervalList_ref.fa
+#hg38 hg38 Human hg38 ${__HERE__}/picard_BedToIntervalList_ref.fa
b
diff -r f6ced08779c4 -r 1cd1cf786389 test-data/err_summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/err_summary Thu May 16 07:13:32 2019 -0400
[
@@ -0,0 +1,12 @@
+## htsjdk.samtools.metrics.StringHeader
+# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Fri May 03 21:58:49 EDT 2019
+
+## METRICS CLASS picard.analysis.artifacts.ErrorSummaryMetrics
+REF_BASE ALT_BASE SUBSTITUTION REF_COUNT ALT_COUNT SUBSTITUTION_RATE
+A C A>C 3877 0 0
+A G A>G 3877 2 0.000516
+A T A>T 3877 0 0
+
+
b
diff -r f6ced08779c4 -r 1cd1cf786389 test-data/pos_details
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pos_details Thu May 16 07:13:32 2019 -0400
[
@@ -0,0 +1,24 @@
+## htsjdk.samtools.metrics.StringHeader
+# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Fri May 03 21:58:49 EDT 2019
+
+## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasDetailMetrics
+SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE CONTEXT FWD_CXT_REF_BASES FWD_CXT_ALT_BASES REV_CXT_REF_BASES REV_CXT_ALT_BASES FWD_ERROR_RATE REV_ERROR_RATE ERROR_RATE QSCORE
+sample-a tumor-a A C AAA 58 0 857 0 0 0 0 100
+sample-a tumor-a A C AAC 234 0 139 0 0 0 0 100
+sample-a tumor-a A C AAG 52 0 265 0 0 0 0 100
+sample-a tumor-a A C AAT 240 0 1358 0 0 0 0 100
+sample-a tumor-a A C CAA 101 0 573 0 0 0 0 100
+sample-a tumor-a A G AAA 58 0 857 1 0 0.001166 0 100
+sample-a tumor-a A G AAC 234 1 139 0 0.004255 0 0.004255 24
+sample-a tumor-a A G AAG 52 0 265 0 0 0 0 100
+sample-a tumor-a A G AAT 240 0 1358 0 0 0 0 100
+sample-a tumor-a A G CAA 101 0 573 0 0 0 0 100
+sample-a tumor-a A T AAA 58 0 857 0 0 0 0 100
+sample-a tumor-a A T AAC 234 0 139 0 0 0 0 100
+sample-a tumor-a A T AAG 52 0 265 0 0 0 0 100
+sample-a tumor-a A T AAT 240 0 1358 0 0 0 0 100
+sample-a tumor-a A T CAA 101 0 573 0 0 0 0 100
+
+
b
diff -r f6ced08779c4 -r 1cd1cf786389 test-data/pos_summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pos_summary Thu May 16 07:13:32 2019 -0400
[
@@ -0,0 +1,21 @@
+## htsjdk.samtools.metrics.StringHeader
+# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Fri May 03 21:58:49 EDT 2019
+
+## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasSummaryMetrics
+SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE TOTAL_QSCORE WORST_CXT WORST_CXT_QSCORE WORST_PRE_CXT WORST_PRE_CXT_QSCORE WORST_POST_CXT WORST_POST_CXT_QSCORE ARTIFACT_NAME
+sample-a tumor-a A C 35 TAA 26 CAN 34 NAA 28 NA
+sample-a tumor-a A G 16 TAT 9 TAN 11 NAT 12 NA
+sample-a tumor-a A T 100 AAA 100 AAN 100 NAA 100 NA
+sample-a tumor-a C A 100 ACA 100 ACN 100 NCA 100 Cref
+sample-a tumor-a C G 100 ACA 100 ACN 100 NCA 100 NA
+sample-a tumor-a C T 100 TCA 29 ACN 100 NCA 34 NA
+sample-a tumor-a G A 34 CGA 23 AGN 28 NGA 30 NA
+sample-a tumor-a G C 36 TGC 26 TGN 30 NGC 30 NA
+sample-a tumor-a G T 36 TGG 25 TGN 30 NGG 30 Gref
+sample-a tumor-a T A 100 ATA 100 ATN 100 NTA 100 NA
+sample-a tumor-a T C 100 GTA 24 CTN 29 NTG 30 NA
+sample-a tumor-a T G 100 ATA 100 ATN 100 NTA 100 NA
+
+
b
diff -r f6ced08779c4 -r 1cd1cf786389 test-data/pre_details
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pre_details Thu May 16 07:13:32 2019 -0400
[
@@ -0,0 +1,24 @@
+## htsjdk.samtools.metrics.StringHeader
+# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Fri May 03 21:58:49 EDT 2019
+
+## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterDetailMetrics
+SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE CONTEXT PRO_REF_BASES PRO_ALT_BASES CON_REF_BASES CON_ALT_BASES ERROR_RATE QSCORE
+sample-a tumor-a A C AAA 512 0 403 0 0 100
+sample-a tumor-a A C AAC 174 0 199 0 0 100
+sample-a tumor-a A C AAG 168 0 149 0 0 100
+sample-a tumor-a A C AAT 861 0 737 0 0 100
+sample-a tumor-a A C CAA 371 0 303 0 0 100
+sample-a tumor-a A G AAA 512 0 403 1 0 100
+sample-a tumor-a A G AAC 174 0 199 1 0 100
+sample-a tumor-a A G AAG 168 0 149 0 0 100
+sample-a tumor-a A G AAT 861 0 737 0 0 100
+sample-a tumor-a A G CAA 371 0 303 0 0 100
+sample-a tumor-a A T AAA 512 0 403 0 0 100
+sample-a tumor-a A T AAC 174 0 199 0 0 100
+sample-a tumor-a A T AAG 168 0 149 0 0 100
+sample-a tumor-a A T AAT 861 0 737 0 0 100
+sample-a tumor-a A T CAA 371 0 303 0 0 100
+
+
b
diff -r f6ced08779c4 -r 1cd1cf786389 test-data/pre_summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pre_summary Thu May 16 07:13:32 2019 -0400
[
@@ -0,0 +1,21 @@
+## htsjdk.samtools.metrics.StringHeader
+# CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=30 MINIMUM_MAPPING_QUALITY=20 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 CONTEXTS_TO_PRINT=[AAA, CAA, AAC, AAT, AAG] INPUT=test-data/picard_ARRG_test1.bam OUTPUT=OutPut ASSUME_SORTED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false REFERENCE_SEQUENCE=test-data/picard_BedToIntervalList_ref.fa GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false   
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Fri May 03 21:58:49 EDT 2019
+
+## METRICS CLASS picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterSummaryMetrics
+SAMPLE_ALIAS LIBRARY REF_BASE ALT_BASE TOTAL_QSCORE WORST_CXT WORST_CXT_QSCORE WORST_PRE_CXT WORST_PRE_CXT_QSCORE WORST_POST_CXT WORST_POST_CXT_QSCORE ARTIFACT_NAME
+sample-a tumor-a A C 100 CAC 31 CAN 36 NAC 35 NA
+sample-a tumor-a A G 100 GAG 28 GAN 33 NAG 31 NA
+sample-a tumor-a A T 100 AAA 100 AAN 100 NAA 100 NA
+sample-a tumor-a C A 39 CCA 27 CCN 33 NCA 33 NA
+sample-a tumor-a C G 100 ACA 100 ACN 100 NCA 100 NA
+sample-a tumor-a C T 100 GCT 27 GCN 33 NCT 33 Deamination
+sample-a tumor-a G A 42 CGA 27 CGN 33 NGA 31 NA
+sample-a tumor-a G C 39 TGC 29 TGN 33 NGC 33 NA
+sample-a tumor-a G T 100 AGA 100 AGN 100 NGA 100 OxoG
+sample-a tumor-a T A 100 ATA 100 ATN 100 NTA 100 NA
+sample-a tumor-a T C 27 ATA 19 ATN 23 NTA 22 NA
+sample-a tumor-a T G 100 TTA 30 TTN 35 NTA 37 NA
+
+
b
diff -r f6ced08779c4 -r 1cd1cf786389 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu May 16 07:13:32 2019 -0400
b
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of Picard dict file and other files -->
+    <table name="picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/picard_indexes.loc" />
+    </table>
+</tables>