| Next changeset 1:ef0443c0eaba (2022-08-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0" |
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added:
macros.xml sam2rma.xml test-data/13-1941-6_S4_L001_R1_600000.fastq.gz test-data/13-1941-6_S4_L001_R2_600000.fastq.gz test-data/blast_R1.txt test-data/blast_R2.txt test-data/contaminants.txt test-data/daa2info_output1.txt test-data/daa2info_output2.txt test-data/daa2info_output_summary2.txt test-data/input.daa test-data/input1.sam test-data/input2.sam test-data/input_meganized.daa test-data/kegg_output.txt test-data/read_extractor_input.rma6 test-data/read_extractor_output.txt test-data/taxonomy_output.txt |
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| diff -r 000000000000 -r 4f0a8e401e2e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Dec 11 11:52:57 2021 +0000 |
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| b'@@ -0,0 +1,140 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">6.21.7</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">20.09</token>\n+ <xml name="bio_tools">\n+ <xrefs>\n+ <xref type="bio.tools">megan</xref>\n+ </xrefs>\n+ </xml>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">megan</requirement>\n+ </requirements>\n+ </xml>\n+ <macro name="input_type_cond">\n+ <conditional name="input_type_cond">\n+ <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">\n+ <option value="single" selected="true">Single dataset</option>\n+ <option value="pair">Dataset pair</option>\n+ <option value="paired">List of dataset pairs</option>\n+ </param>\n+ <when value="single">\n+ <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>\n+ <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>\n+ </when>\n+ <when value="pair">\n+ <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>\n+ <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by Blast to generate the Blast file below"/>\n+ <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>\n+ <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>\n+ <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/>\n+ </when>\n+ <when value="paired">\n+ <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>\n+ <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>\n+ <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/>\n+ <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/>\n+ </when>\n+ </conditional>\n+ </macro>\n+ <macro name="input_daa_param">\n+ <param argument="--in" type="data" format="daa" label="Input DAA file"/>\n+ </macro>\n+ <macro name="long_reads_param">\n+ <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>\n+ </macro>\n+ <macro name="max_matches_per_read_param">\n+ <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>\n+ </macro>\n+ <macro name="only_named_classifications_param">\n+ <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">\n+ <sanitizer>\n+ <valid initial="@VALIDINITIAL@">\n+ <remove value="'" />\n+ <add value="|" />\n+ </valid>\n+ <mapping initial="none">\n+ <add source="'" targe'..b'"KEGG">KEGG</option>\n+ <option value="SEED">SEED</option>\n+ <option value="Taxonomy">Taxonomy</option>\n+ </macro>\n+ <macro name="blast_mode_options">\n+ <option value="Unknown" selected="true">Unknown</option>\n+ <option value="BlastN">BlastN</option>\n+ <option value="BlastP">BlastP</option>\n+ <option value="BlastX">BlastX</option>\n+ <option value="Classifier">Classifier</option>\n+ </macro>\n+ <macro name="classify_param">\n+ <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>\n+ </macro>\n+ <macro name="min_score_param">\n+ <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>\n+ </macro>\n+ <macro name="max_expected_param">\n+ <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>\n+ </macro>\n+ <macro name="min_percent_identity_param">\n+ <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>\n+ </macro>\n+ <macro name="top_percent_param">\n+ <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>\n+ </macro>\n+ <macro name="min_max_params">\n+ <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>\n+ <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>\n+ <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>\n+ <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>\n+ <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>\n+ </macro>\n+ <macro name="lca_params">\n+ <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">\n+ <option value="naive" selected="true">naive</option>\n+ <option value="weighted">weighted</option>\n+ <option value="longReads">longReads</option>\n+ </param>\n+ <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>\n+ </macro>\n+ <macro name="read_assignment_mode_param">\n+ <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">\n+ <option value="alignedBases" selected="true">alignedBases</option>\n+ <option value="readCount">readCount</option>\n+ </param>\n+ </macro>\n+ <macro name="con_file_param">\n+ <param argument="--conFile" type="data" format="txt" optional="true" label="File of contaminant taxa (one id or name per line)" help="Optional, no selection ignores"/>\n+ </macro>\n+ <macro name="mapdb_param">\n+ <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>\n+ </macro>\n+ <xml name="sanitize_query" token_validinitial="string.printable">\n+ <sanitizer>\n+ <valid initial="@VALIDINITIAL@">\n+ <remove value="'" />\n+ <add value="|" />\n+ </valid>\n+ <mapping initial="none">\n+ <add source="'" target="'"'"'" />\n+ </mapping>\n+ </sanitizer>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/nmeth.3176</citation>\n+ <citation type="doi">10.1101/gr.120618.111</citation>\n+ <citation type="doi">10.1101/gr.5969107</citation>\n+ </citations>\n+ </xml>\n+</macros>\n+\n' |
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| diff -r 000000000000 -r 4f0a8e401e2e sam2rma.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam2rma.xml Sat Dec 11 11:52:57 2021 +0000 |
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| b'@@ -0,0 +1,249 @@\n+<tool id="megan_sam2rma" name="MEGAN: Generate a MEGAN rma6 file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>from a DIAMOND or MALT sam file</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="bio_tools"/>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+#import re\n+\n+#if str($input_type_cond.input_type) in [\'single\', \'pair\']:\n+ #set read1 = $input_type_cond.read1\n+ #set sam1 = $input_type_cond.sam1\n+#else:\n+ ## Processing paired reads are tricky if we\'re\n+ ## downstream from MALT. MALT doesn\xe2\x80\x99t have a\n+ ## paired-read mode, so it won\xe2\x80\x99t attempt to analyze\n+ ## reads in pairs. To do paired read processing,\n+ ## set MALT to generate SAM files and then import the\n+ ## SAM files into MEGAN, specifying paired read mode\n+ ## there. If you have multiple SAM files for the same\n+ ## sample, then import them all at the same time to\n+ ## create one unified rma6 file.\n+\n+ #set read1 = $input_type_cond.reads_collection[\'forward\']\n+ #set sam1 = $input_type_cond.sam1\n+#end if\n+\n+#if $read1.is_of_type(\'fasta\', \'fasta.gz\'):\n+ #set read_ext = \'.fasta\'\n+#else:\n+ #set read_ext = \'.fastq\'\n+#end if\n+#if $read1.ext.endswith(\'.gz\'):\n+ #set read_ext = $read_ext + \'.gz\'\n+#end if\n+\n+#set read1_identifier = \'read1\' + $read_ext\n+ln -s \'${read1}\' \'${read1_identifier}\' &&\n+\n+#set sam1_identifier = \'sam1.\' + $sam1.ext\n+ln -s \'${sam1}\' \'${sam1_identifier}\' &&\n+\n+#if str($input_type_cond.input_type) in [\'pair\', \'paired\']:\n+ #if str($input_type_cond.input_type) == \'pair\':\n+ #set read2 = $input_type_cond.read2\n+ #set sam2 = $input_type_cond.sam2\n+ #else if str($input_type_cond.input_type) == \'paired\':\n+ #set read2 = $input_type_cond.reads_collection[\'reverse\']\n+ #set sam2 = $input_type_cond.sam2\n+ #end if\n+ #set read2_identifier = \'read2\' + $read_ext\n+ ln -s \'${read2}\' \'${read2_identifier}\' &&\n+ #set sam2_identifier = \'sam2.\' + $sam2.ext\n+ ln -s \'${sam2}\' \'${sam2_identifier}\' &&\n+#end if\n+\n+## The output must be a directory when we have multiple\n+## inputs, and the outputs inherit the base name of the\n+## inputs.\n+\n+sam2rma\n+#if str($input_type_cond.input_type) == \'single\':\n+ --in \'${sam1_identifier}\'\n+ --reads \'${read1_identifier}\'\n+ --out \'${output_single}\'\n+#else if str($input_type_cond.input_type) == \'pair\':\n+ --in \'${sam1_identifier}\' \'${sam2_identifier}\'\n+ --reads \'${read1_identifier}\' \'${read2_identifier}\'\n+ --paired\n+ --pairedSuffixLength $input_type_cond.pairedSuffixLength \n+ --out \'.\'\n+#else if str($input_type_cond.input_type) == \'paired\':\n+ --in \'${sam1_identifier}\' \'${sam2_identifier}\'\n+ --reads \'${read1_identifier}\' \'${read2_identifier}\'\n+ --paired\n+ --pairedSuffixLength $input_type_cond.pairedSuffixLength \n+ ## Strangely, megan requires an output\n+ ## directory when processing paired reads\n+ ## even though it produces a single file.\n+ ## We\'ll accommodate thie by prepending ./\n+ ## to a temporary output file and then move\n+ ## it later.\n+ --out \'.\'\n+#end if\n+#if $advanced_options.metaDataFile:\n+ --metaDataFile \'$advanced_options.metaDataFile\'\n+#end if\n+#if str($advanced_options.paired_reads_cond.paired_reads) == \'yes\':\n+ --paired\n+ $advanced_options.paired_reads_cond.pairedSuffixLength\n+#end if\n+$advanced_options.longReads\n+--maxMatchesPerRead $advanced_options.maxMatchesPerRead\n+$advanced_options.classify\n+--minScore $advanced_options.minScore\n+--maxExpected $advanced_options.maxExpected\n+--topPercent $advanced_options.topPercent\n+--minSupportPercent $advanced_options.minSupportPercent\n+--minSupport $advanced_options.minSupport\n+--minPercentReadCover $advanced_options.minPercentReadCover\n+--minPercentReferenceCover $advanced_options.minPercentReferenceCover\n+--minReadLength $advanced_options.minReadLength\n+--lcaAlgorithm \'$advanced_opt'..b'\n+ <expand macro="max_matches_per_read_param"/>\n+ <expand macro="classify_param"/>\n+ <expand macro="min_score_param"/>\n+ <expand macro="max_expected_param"/>\n+ <expand macro="top_percent_param"/>\n+ <expand macro="min_max_params"/>\n+ <expand macro="lca_params"/>\n+ <expand macro="read_assignment_mode_param"/>\n+ <expand macro="con_file_param"/>\n+ <expand macro="mapdb_param"/>\n+ <expand macro="only_named_classifications_param"/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="output_single" format="rma6">\n+ <filter>input_type_cond[\'input_type\'] == \'single\'</filter>\n+ </data>\n+ <data name="output_forward" format="rma6" label="${tool.name} on ${on_string} (forward">\n+ <filter>input_type_cond[\'input_type\'] != \'single\'</filter>\n+ </data>\n+ <data name="output_reverse" format="rma6" label="${tool.name} on ${on_string} (reverse)">\n+ <filter>input_type_cond[\'input_type\'] != \'single\'</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <!-- Single dataset input -->\n+ <test expect_num_outputs="1">\n+ <param name="sam1" ftype="sam" value="input1.sam"/>\n+ <param name="read1" ftype="fastqsanger.gz" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>\n+ <output name="output_single" ftype="rma6">\n+ <assert_contents>\n+ <has_size value="885"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Dataset pair input -->\n+ <test expect_num_outputs="2">\n+ <param name="input_type" value="pair"/>\n+ <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="sam1" value="input1.sam" ftype="sam"/>\n+ <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="sam2" value="input2.sam" ftype="sam"/>\n+ <output name="output_forward" ftype="rma6">\n+ <assert_contents>\n+ <has_size value="805"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_reverse" ftype="rma6">\n+ <assert_contents>\n+ <has_size value="805"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- List of dataset pairs input -->\n+ <test expect_num_outputs="2">\n+ <param name="input_type" value="paired"/>\n+ <param name="reads_collection">\n+ <collection type="paired">\n+ <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>\n+ <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>\n+ </collection>\n+ </param>\n+ <param name="sam1" value="input1.sam" ftype="sam"/>\n+ <param name="sam2" value="input2.sam" ftype="sam"/>\n+ <output name="output_forward" ftype="rma6">\n+ <assert_contents>\n+ <has_size value="805"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_reverse" ftype="rma6">\n+ <assert_contents>\n+ <has_size value="805"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+Generates a MEGAN RMA (RealMedia Audio) file from a SAM file that was generated by DIAMOND or MALT. MEGAN uses an\n+update of the original RMA file format known as RMA6.\n+\n+Inputs consist of reads in fasta or fasqsanger format (gzip compression is supported) and associated SAM files.\n+Each read file should have been used previously as the input to DIAMOND or MALT to produce the associated SAM file\n+for this tool.\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 4f0a8e401e2e test-data/blast_R1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast_R1.txt Sat Dec 11 11:52:57 2021 +0000 |
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| @@ -0,0 +1,404 @@ +BLASTN output produced by MALT + + +Query= XXXXXXXXXX:7:1101:1582:1835#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1610:1859#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1743:1871#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1878#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2990:100153#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1624:1906#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1666:1926#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2921:100163#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1513:1929#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2759:100170#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1708:1937#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2981:100211#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1688:1946#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2767:100225#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1959#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2797:100234#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1552:1976#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1748:1978#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2779:100239#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1593:1980#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2946:100242#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1987:1781#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3046:100006#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1900:1788#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3214:100027#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1848:1879#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3237:100032#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3027:100049#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1756:1891#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3238:100065#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1915:1901#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100082#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1964:1931#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3088:100091#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1840:1948#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3105:100094#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1958:1952#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3190:100106#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1993:1999#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3117:100110#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2159:1798#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3147:100111#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2152:1838#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3065:100152#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2180:1843#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3154:100159#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2125:1861#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100173#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2076:1911#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3166:100190#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2196:1920#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3225:100207#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2115:1927#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3019:100219#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2179:1937#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3202:100230#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2149:1945#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3211:100242#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2169:1964#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3168:100244#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3005:100246#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2313:1789#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3253:100014#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2361:1794#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2337:1794#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3284:100039#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2477:1795#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3310:100056#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2355:1821#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3420:100060#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2418:1834#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3267:100061#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2378:1838#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3416:100083#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2481:1853#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3411:100111#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3258:100128#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2252:1856#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3428:100129#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1871#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3387:100138#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2269:1904#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3444:100163#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2259:1943#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3371:100179#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2371:1957#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3311:100186#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1961#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3438:100192#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2333:1962#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3479:100209#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2459:1990#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3417:100210#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2372:1994#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3452:100214#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2677:1830#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3354:100219#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2603:1846#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3600:100019#/1 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2535:1848#/1 + +***** No hits found ****** + +EOF |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/blast_R2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast_R2.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,404 @@ +BLASTN output produced by MALT + + +Query= XXXXXXXXXX:7:1101:1582:1835#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1610:1859#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1743:1871#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1878#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2990:100153#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1624:1906#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1666:1926#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2921:100163#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1513:1929#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2759:100170#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1708:1937#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2981:100211#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1688:1946#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2767:100225#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1536:1959#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2797:100234#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1552:1976#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1748:1978#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2779:100239#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1593:1980#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2946:100242#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1987:1781#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3046:100006#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1900:1788#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3214:100027#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1848:1879#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3237:100032#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3027:100049#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1756:1891#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3238:100065#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1915:1901#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100082#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1964:1931#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3088:100091#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1840:1948#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3105:100094#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1958:1952#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3190:100106#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:1993:1999#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3117:100110#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2159:1798#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3147:100111#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2152:1838#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3065:100152#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2180:1843#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3154:100159#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2125:1861#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3198:100173#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2076:1911#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3166:100190#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2196:1920#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3225:100207#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2115:1927#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3019:100219#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2179:1937#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3202:100230#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2149:1945#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3211:100242#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2169:1964#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3168:100244#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3005:100246#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2313:1789#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3253:100014#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2361:1794#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2337:1794#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3284:100039#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2477:1795#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3310:100056#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2355:1821#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3420:100060#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2418:1834#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3267:100061#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2378:1838#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3416:100083#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2481:1853#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3411:100111#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3258:100128#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2252:1856#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3428:100129#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1871#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3387:100138#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2269:1904#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3444:100163#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2259:1943#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3371:100179#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2371:1957#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3311:100186#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2394:1961#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3438:100192#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2333:1962#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3479:100209#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2459:1990#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3417:100210#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2372:1994#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3452:100214#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2677:1830#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3354:100219#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2603:1846#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:3600:100019#/2 + +***** No hits found ****** + +Query= XXXXXXXXXX:7:1101:2535:1848#/2 + +***** No hits found ****** + +EOF |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/contaminants.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contaminants.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +Illumina Single End Adapter 1 ACACTCTTTCCCTACACGACGCTGTTCCATCT +Illumina Single End Adapter 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT +Illumina Single End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Single End PCR Primer 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT +Illumina Single End Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT + +Illumina Paired End Adapter 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Paired End Adapter 2 CTCGGCATTCCTGCTGAACCGCTCTTCCGATCT +Illumina Paried End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Paired End PCR Primer 2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT +Illumina Paried End Sequencing Primer 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT +Illumina Paired End Sequencing Primer 2 CGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/daa2info_output1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/daa2info_output1.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,3 @@ +# Number of reads: 1 +# Alignment mode: BLASTP +# Is meganized: false |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/daa2info_output2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/daa2info_output2.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,19 @@ +# Number of reads: 1 +# Alignment mode: BLASTP +# Is meganized: true +# Classifications: Taxonomy +# Meganization summary: +## @Creator DAA2Info +## @CreationDate +## @ContentType Summary4 +## @Names input +## @BlastMode BlastP +## @Uids +## @Sizes 1.0 +## @TotalReads 1 +## @AdditionalReads 0 +## Classifications: +## Taxonomy (1 classes) +## @Algorithm Taxonomy merge +## @Parameters +## |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/daa2info_output_summary2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/daa2info_output_summary2.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,16 @@ +@Creator DAA2Info +@CreationDate +@ContentType Summary4 +@Names input +@BlastMode BlastP +@Uids +@Sizes 1 +@TotalReads 1 +@AdditionalReads 0 +@Algorithm Taxonomy merge +@Parameters +@ColorTable Fews8 White-Green +TAX -2 1 +END_OF_DATA_TABLE +#SampleID @Source +input.daa input.DAA |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/input.daa |
| b |
| Binary file test-data/input.daa has changed |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/input1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.sam Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.5 SO:unsorted GO:query +@PG ID:1 PN:MALT CL:--mode BlastN --matchScore 2 --mismatchScore -3 --setLambda 0.625 --setK 0.41 --alignmentType Local --inFile 13-1941-6_S4_L001_R1_600000_fastq_gz.fastq.gz --index /home/galaxy/tool-data/malt_index/AF2122-1 --output ./output.rma6 --numThreads 1 --memoryMode load --maxTables 0 --minBitScore 50.0 --maxExpected 1.0 --minPercentIdentity 0.0 --maxAlignmentsPerQuery 25 --maxAlignmentsPerRef 1 --topPercent 10.0 --minSupportPercent 0.001 --minSupport 0 --minPercentIdentityLCA 0.0 --maxSeedsPerFrame 100 --maxSeedsPerRef 20 --seedShift 1 --gapOpen 11 --gapExtend 1 --band 4 --alignments ./alignments_output.SAM.gz --format SAM --outAligned ./aligned_output.fna.gz --outUnaligned ./unaligned_output.fna.gz DS:BlastN +@RG ID:1 PL:unknown SM:unknown +@CO BlastN-like alignments +@CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/input2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input2.sam Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,5 @@ +@HD VN:1.5 SO:unsorted GO:query +@PG ID:1 PN:MALT CL:--mode BlastN --matchScore 2 --mismatchScore -3 --setLambda 0.625 --setK 0.41 --alignmentType Local --inFile 13-1941-6_S4_L001_R2_600000_fastq_gz.fastq.gz --index /home/galaxy/tool-data/malt_index/AF2122-1 --output ./output.rma6 --numThreads 1 --memoryMode load --maxTables 0 --minBitScore 50.0 --maxExpected 1.0 --minPercentIdentity 0.0 --maxAlignmentsPerQuery 25 --maxAlignmentsPerRef 1 --topPercent 10.0 --minSupportPercent 0.001 --minSupport 0 --minPercentIdentityLCA 0.0 --maxSeedsPerFrame 100 --maxSeedsPerRef 20 --seedShift 1 --gapOpen 11 --gapExtend 1 --band 4 --alignments ./alignments_output.SAM.gz --format SAM --outAligned ./aligned_output.fna.gz --outUnaligned ./unaligned_output.fna.gz DS:BlastN +@RG ID:1 PL:unknown SM:unknown +@CO BlastN-like alignments +@CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/input_meganized.daa |
| b |
| Binary file test-data/input_meganized.daa has changed |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/kegg_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kegg_output.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,100 @@ +XXXXXXXXXX:7:1101:1582:1835#/1; ; +XXXXXXXXXX:7:1101:1610:1859#/1; ; +XXXXXXXXXX:7:1101:1743:1871#/1; ; +XXXXXXXXXX:7:1101:1536:1878#/1; ; +XXXXXXXXXX:7:1101:2990:100153#/1; ; +XXXXXXXXXX:7:1101:1624:1906#/1; ; +XXXXXXXXXX:7:1101:1666:1926#/1; ; +XXXXXXXXXX:7:1101:2921:100163#/1; ; +XXXXXXXXXX:7:1101:1513:1929#/1; ; +XXXXXXXXXX:7:1101:2759:100170#/1; ; +XXXXXXXXXX:7:1101:1708:1937#/1; ; +XXXXXXXXXX:7:1101:2981:100211#/1; ; +XXXXXXXXXX:7:1101:1688:1946#/1; ; +XXXXXXXXXX:7:1101:2767:100225#/1; ; +XXXXXXXXXX:7:1101:1536:1959#/1; ; +XXXXXXXXXX:7:1101:2797:100234#/1; ; +XXXXXXXXXX:7:1101:1552:1976#/1; ; +XXXXXXXXXX:7:1101:1748:1978#/1; ; +XXXXXXXXXX:7:1101:2779:100239#/1; ; +XXXXXXXXXX:7:1101:1593:1980#/1; ; +XXXXXXXXXX:7:1101:2946:100242#/1; ; +XXXXXXXXXX:7:1101:1987:1781#/1; ; +XXXXXXXXXX:7:1101:3046:100006#/1; ; +XXXXXXXXXX:7:1101:1900:1788#/1; ; +XXXXXXXXXX:7:1101:3214:100027#/1; ; +XXXXXXXXXX:7:1101:1848:1879#/1; ; +XXXXXXXXXX:7:1101:3237:100032#/1; ; +XXXXXXXXXX:7:1101:3027:100049#/1; ; +XXXXXXXXXX:7:1101:1756:1891#/1; ; +XXXXXXXXXX:7:1101:3238:100065#/1; ; +XXXXXXXXXX:7:1101:1915:1901#/1; ; +XXXXXXXXXX:7:1101:3198:100082#/1; ; +XXXXXXXXXX:7:1101:1964:1931#/1; ; +XXXXXXXXXX:7:1101:3088:100091#/1; ; +XXXXXXXXXX:7:1101:1840:1948#/1; ; +XXXXXXXXXX:7:1101:3105:100094#/1; ; +XXXXXXXXXX:7:1101:1958:1952#/1; ; +XXXXXXXXXX:7:1101:3190:100106#/1; ; +XXXXXXXXXX:7:1101:1993:1999#/1; ; +XXXXXXXXXX:7:1101:3117:100110#/1; ; +XXXXXXXXXX:7:1101:2159:1798#/1; ; +XXXXXXXXXX:7:1101:3147:100111#/1; ; +XXXXXXXXXX:7:1101:2152:1838#/1; ; +XXXXXXXXXX:7:1101:3065:100152#/1; ; +XXXXXXXXXX:7:1101:2180:1843#/1; ; +XXXXXXXXXX:7:1101:3154:100159#/1; ; +XXXXXXXXXX:7:1101:2125:1861#/1; ; +XXXXXXXXXX:7:1101:3198:100173#/1; ; +XXXXXXXXXX:7:1101:2076:1911#/1; ; +XXXXXXXXXX:7:1101:3166:100190#/1; ; +XXXXXXXXXX:7:1101:2196:1920#/1; ; +XXXXXXXXXX:7:1101:3225:100207#/1; ; +XXXXXXXXXX:7:1101:2115:1927#/1; ; +XXXXXXXXXX:7:1101:3019:100219#/1; ; +XXXXXXXXXX:7:1101:2179:1937#/1; ; +XXXXXXXXXX:7:1101:3202:100230#/1; ; +XXXXXXXXXX:7:1101:2149:1945#/1; ; +XXXXXXXXXX:7:1101:3211:100242#/1; ; +XXXXXXXXXX:7:1101:2169:1964#/1; ; +XXXXXXXXXX:7:1101:3168:100244#/1; ; +XXXXXXXXXX:7:1101:3005:100246#/1; ; +XXXXXXXXXX:7:1101:2313:1789#/1; ; +XXXXXXXXXX:7:1101:3253:100014#/1; ; +XXXXXXXXXX:7:1101:2361:1794#/1; ; +XXXXXXXXXX:7:1101:2337:1794#/1; ; +XXXXXXXXXX:7:1101:3284:100039#/1; ; +XXXXXXXXXX:7:1101:2477:1795#/1; ; +XXXXXXXXXX:7:1101:3310:100056#/1; ; +XXXXXXXXXX:7:1101:2355:1821#/1; ; +XXXXXXXXXX:7:1101:3420:100060#/1; ; +XXXXXXXXXX:7:1101:2418:1834#/1; ; +XXXXXXXXXX:7:1101:3267:100061#/1; ; +XXXXXXXXXX:7:1101:2378:1838#/1; ; +XXXXXXXXXX:7:1101:3416:100083#/1; ; +XXXXXXXXXX:7:1101:2481:1853#/1; ; +XXXXXXXXXX:7:1101:3411:100111#/1; ; +XXXXXXXXXX:7:1101:3258:100128#/1; ; +XXXXXXXXXX:7:1101:2252:1856#/1; ; +XXXXXXXXXX:7:1101:3428:100129#/1; ; +XXXXXXXXXX:7:1101:2394:1871#/1; ; +XXXXXXXXXX:7:1101:3387:100138#/1; ; +XXXXXXXXXX:7:1101:2269:1904#/1; ; +XXXXXXXXXX:7:1101:3444:100163#/1; ; +XXXXXXXXXX:7:1101:2259:1943#/1; ; +XXXXXXXXXX:7:1101:3371:100179#/1; ; +XXXXXXXXXX:7:1101:2371:1957#/1; ; +XXXXXXXXXX:7:1101:3311:100186#/1; ; +XXXXXXXXXX:7:1101:2394:1961#/1; ; +XXXXXXXXXX:7:1101:3438:100192#/1; ; +XXXXXXXXXX:7:1101:2333:1962#/1; ; +XXXXXXXXXX:7:1101:3479:100209#/1; ; +XXXXXXXXXX:7:1101:2459:1990#/1; ; +XXXXXXXXXX:7:1101:3417:100210#/1; ; +XXXXXXXXXX:7:1101:2372:1994#/1; ; +XXXXXXXXXX:7:1101:3452:100214#/1; ; +XXXXXXXXXX:7:1101:2677:1830#/1; ; +XXXXXXXXXX:7:1101:3354:100219#/1; ; +XXXXXXXXXX:7:1101:2603:1846#/1; ; +XXXXXXXXXX:7:1101:3600:100019#/1; ; +XXXXXXXXXX:7:1101:2535:1848#/1; ; |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/read_extractor_input.rma6 |
| b |
| Binary file test-data/read_extractor_input.rma6 has changed |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/read_extractor_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read_extractor_output.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>sequence +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY |
| b |
| diff -r 000000000000 -r 4f0a8e401e2e test-data/taxonomy_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy_output.txt Sat Dec 11 11:52:57 2021 +0000 |
| b |
| @@ -0,0 +1,100 @@ +XXXXXXXXXX:7:1101:1582:1835#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1610:1859#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1743:1871#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1536:1878#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2990:100153#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1624:1906#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1666:1926#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2921:100163#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1513:1929#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2759:100170#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1708:1937#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2981:100211#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1688:1946#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2767:100225#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1536:1959#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2797:100234#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1552:1976#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1748:1978#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2779:100239#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1593:1980#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2946:100242#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1987:1781#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3046:100006#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1900:1788#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3214:100027#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1848:1879#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3237:100032#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3027:100049#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1756:1891#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3238:100065#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1915:1901#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3198:100082#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1964:1931#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3088:100091#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1840:1948#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3105:100094#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1958:1952#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3190:100106#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:1993:1999#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3117:100110#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2159:1798#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3147:100111#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2152:1838#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3065:100152#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2180:1843#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3154:100159#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2125:1861#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3198:100173#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2076:1911#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3166:100190#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2196:1920#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3225:100207#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2115:1927#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3019:100219#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2179:1937#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3202:100230#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2149:1945#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3211:100242#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2169:1964#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3168:100244#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3005:100246#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2313:1789#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3253:100014#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2361:1794#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2337:1794#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3284:100039#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2477:1795#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3310:100056#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2355:1821#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3420:100060#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2418:1834#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3267:100061#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2378:1838#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3416:100083#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2481:1853#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3411:100111#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3258:100128#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2252:1856#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3428:100129#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2394:1871#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3387:100138#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2269:1904#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3444:100163#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2259:1943#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3371:100179#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2371:1957#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3311:100186#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2394:1961#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3438:100192#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2333:1962#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3479:100209#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2459:1990#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3417:100210#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2372:1994#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3452:100214#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2677:1830#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3354:100219#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2603:1846#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:3600:100019#/1; ; No hits; 100; +XXXXXXXXXX:7:1101:2535:1848#/1; ; No hits; 100; |