| Next changeset 1:11e5408fd238 (2017-04-04) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit 2645abbd04dd68266f995b8259e991c31388cda8 |
|
added:
all_fasta.loc.sample pilon.xml test-data/test1-vcf-part test-data/test1.bam test-data/test1.fasta tool_data_table_conf.xml.sample |
| b |
| diff -r 000000000000 -r fe0dc27e6327 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sat Aug 13 04:50:55 2016 -0400 |
| b |
| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
| b |
| diff -r 000000000000 -r fe0dc27e6327 pilon.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pilon.xml Sat Aug 13 04:50:55 2016 -0400 |
| [ |
| b'@@ -0,0 +1,317 @@\n+<tool id="pilon" name="pilon" version="0.1">\n+ <description>An automated genome assembly improvement and variant detection tool</description>\n+ <requirements>\n+ <requirement type="package" version="1.18">pilon</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $auto_selection.auto_enabled == "yes"\n+ #for $bamfile in $auto_selection.bam\n+ ln -f -s "$bamfile" "\\$(basename $bamfile)" &&\n+ ln -f -s "$bamfile.metadata.bam_index" "\\$(basename $bamfile).bai" &&\n+ #end for\n+ #end if\n+ #if $options.selection_mode == "advanced"\n+ #if $options.frags_selection.frags_enabled == "yes"\n+ #for $bamfile in $options.frags_selection.frags\n+ ln -f -s "$bamfile" "\\$(basename $bamfile)" &&\n+ ln -f -s "$bamfile.metadata.bam_index" "\\$(basename $bamfile).bai" &&\n+ #end for\n+ #end if\n+ #if $options.jumps_selection.jumps_enabled == "yes"\n+ #for $bamfile in $options.jumps_selection.jumps\n+ ln -f -s "$bamfile" "\\$(basename $bamfile)" &&\n+ ln -f -s "$bamfile.metadata.bam_index" "\\$(basename $bamfile).bai" &&\n+ #end for\n+ #end if\n+ #if $options.unpaired_selection.unpaired_enabled == "yes"\n+ #for $bamfile in $options.unpaired_selection.unpaired\n+ ln -f -s "$bamfile" "\\$(basename $bamfile)" &&\n+ ln -f -s "$bamfile.metadata.bam_index" "\\$(basename $bamfile).bai" &&\n+ #end for\n+ #end if\n+ #end if\n+ ln -s -f\n+ #if $reference_genome.reference_genome_source == "history"\n+ "$reference_genome.history_item"\n+ #else\n+ "$reference_genome.builtin.fields.path"\n+ #end if\n+ reference.fasta &&\n+ pilon\n+ --genome reference.fasta\n+ $variant\n+ $changes\n+ #if $auto_selection.auto_enabled == "yes"\n+ #for $bamfile in $auto_selection.bam\n+ --bam "\\$(basename $bamfile)"\n+ #end for\n+ #end if\n+ #if $options.selection_mode == "advanced"\n+ #if $options.frags_selection.frags_enabled == "yes"\n+ #for $bamfile in $options.frags_selection.frags\n+ --frags "\\$(basename $bamfile)"\n+ #end for\n+ #end if\n+ #if $options.jumps_selection.jumps_enabled == "yes"\n+ #for $bamfile in $options.jumps_selection.jumps\n+ --jumps "\\$(basename $bamfile)"\n+ #end for\n+ #end if\n+ #if $options.unpaired_selection.unpaired_enabled == "yes"\n+ #for $bamfile in $options.unpaired_selection.unpaired\n+ --unpaired "\\$(basename $bamfile)"\n+ #end for\n+ #end if\n+ $options.vcfqe\n+ $options.vcf\n+ $options.tracks\n+ --chunksize $options.chunk_size\n+ $options.diploid\n+ $options.duplicates\n+ $options.iupac\n+ $options.nonpf\n+ #if len($options.targetlist.strip()) > 0\n+ --targetlist $options.targetlist\n+ #end if\n+ --fix $options.fixes\n+ $options.verbose\n+ --defaultqual $options.defaultqual\n+ --flank $options.flank\n+ --gapmargin $options.gapmargin\n+ --K $options.kmersize\n+ --mindepth $options.mindepth\n+ --mingap $options.mingap\n+ --minmq $options.minmq\n+ --minqual $options.minqual\n+ $options.nostrays\n+ #end if\n+ --threads \\${GALAXY_SLOTS:-1}\n+ --output pilon\n+ ]]></command>\n+ <inputs>\n+ <conditional name="reference_genome">\n+ <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select">\n+ <option selected="True" value="history">Use a genome from history</option>\n+ <option value="builtin">Use a built-in genome"</option>\n+ </param>\n+ <when value="his'..b'asta" name="history_item" value="test1.fasta" />\n+ <param name="bam" value="test1.bam" />\n+ <param name="variant" value="true" />\n+ <param name="selection_mode" value="advanced" />\n+ <param name="tracks" value="true" />\n+ <output file="test1-vcf-part" ftype="vcf" name="output_vcf" compare="contains" />\n+ <output md5="352907b0d965bc926289b1b2eb9cbecb" ftype="fasta" name="output_fasta" />\n+ <output_collection name="tracks">\n+ <element name="output_pilon_bed" md5="ae0518a6d641efecdcf41c808c014226" />\n+ <element name="output_changes_wig" md5="26e0a9a3793e6604673e9911c4d334ab" />\n+ <element name="output_unconfirmed_wig" md5="f8bb3def4547e854bd90e1a6b4f8cc66" />\n+ <element name="output_copynumber_wig" md5="c1e94296fbc24d00fa7d057f30e4de8f" />\n+ <element name="output_coverage_wig" md5="48f7da4bad60fcbb49aaaa992aef8a02" />\n+ <element name="output_badcoverage_wig" md5="31e3ad4a5d0f8cd1e296e4b1424d6a95" />\n+ <element name="output_pctbad_wig" md5="8353134113c87dbc7d9497f983d58b4b" />\n+ <element name="output_deltacoverage_wig" md5="e0fb6474b851e1890f91c57c2ba1fd76" />\n+ <element name="output_dipcoverage_wig" md5="8885c63df1dc7309a7bab371b9eb449b" />\n+ <element name="output_physicalcoverage_wig" md5="db485f84b51499c3a3c72da70a8ef7af" />\n+ <element name="output_clippedalignments_wig" md5="b6eab0827a9b6f2e925d9ece5ee4f87f" />\n+ <element name="output_weightedqual_wig" md5="9987289bd0ec8cd05bd6d330bdd1d01d" />\n+ <element name="output_weightedmq_wig" md5="7ec1b6420f52fc44bf3c04aa593fcdeb" />\n+ <element name="output_gc_wig" md5="815af1378d016b85ed6f52667dde10c1" />\n+ </output_collection>\n+ </test>\n+\n+ </tests>\n+ <help><![CDATA[\n+ Pilon is a software tool which can be used to:\n+\n+ * Automatically improve draft assemblies\n+\n+ * Find variation among strains, including large event detection\n+\n+ Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:\n+\n+ * Single base differences\n+\n+ * Small indels\n+\n+ * Larger indel or block substitution events\n+\n+ * Gap filling\n+\n+ * Identification of local misassemblies, including optional opening of new gaps\n+\n+ Pilon then outputs a FASTA file containing an improved representation of the genome from the read data and an optional VCF file detailing variation seen between the read data and the input genome.\n+\n+ To aid manual inspection and improvement by an analyst, Pilon can optionally produce tracks that can be displayed in genome viewers such as IGV and GenomeView, and it reports other events (such as possible large collapsed repeat regions) in its standard output.\n+\n+ Note on **mindepth**:\n+\n+ Variants (snps and indels) will only be called if there is coverage of good pairs\n+ at the value set for *mindepth* depth or more; if this value is >= 1, it is an absolute depth, if it is a\n+ fraction < 1, then minimum depth is computed by multiplying this value by the mean\n+ coverage for the region, with a minumum value of 5 (default 0.1: min depth to call\n+ is 10% of mean coverage or 5, whichever is greater).\n+\n+ Note on **stray read filtering**\n+\n+ By default a pass is made through the input BAM files to identify stray pairs, that is,\n+ those pairs in which both reads are aligned but not marked valid because they have\n+ inconsistent orientation or separation. Identifying stray pairs can help fill gaps\n+ and assemble larger insertions, especially of repeat content. However, doing so\n+ sometimes consumes considerable memory.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1371/journal.pone.0112963</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r fe0dc27e6327 test-data/test1-vcf-part --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-vcf-part Sat Aug 13 04:50:55 2016 -0400 |
| b |
| b'@@ -0,0 +1,85 @@\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE\n+gi|448814763|ref|NC_000962.3|\t1\t.\tT\t.\t1276\tPASS\tDP=32;TD=65;BQ=40;MQ=46;QD=39;BC=0,0,0,32;QP=0,0,0,100;PC=55;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t2\t.\tT\t.\t1408\tPASS\tDP=36;TD=73;BQ=39;MQ=47;QD=39;BC=0,0,0,36;QP=0,0,0,100;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t3\t.\tG\t.\t1450\tPASS\tDP=37;TD=74;BQ=39;MQ=47;QD=39;BC=0,0,37,0;QP=0,0,100,0;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t4\t.\tA\t.\t1456\tPASS\tDP=37;TD=77;BQ=39;MQ=47;QD=39;BC=37,0,0,0;QP=100,0,0,0;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t5\t.\tC\t.\t1567\tPASS\tDP=39;TD=79;BQ=40;MQ=48;QD=40;BC=0,39,0,0;QP=0,100,0,0;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t6\t.\tC\t.\t1606\tPASS\tDP=40;TD=80;BQ=40;MQ=48;QD=40;BC=0,40,0,0;QP=0,100,0,0;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t7\t.\tG\t.\t1586\tPASS\tDP=40;TD=80;BQ=40;MQ=48;QD=39;BC=0,0,40,0;QP=0,0,100,0;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t8\t.\tA\t.\t1557\tPASS\tDP=40;TD=81;BQ=39;MQ=48;QD=38;BC=40,0,0,0;QP=100,0,0,0;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t9\t.\tT\t.\t1641\tPASS\tDP=42;TD=84;BQ=39;MQ=48;QD=39;BC=0,0,0,42;QP=0,0,0,100;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t10\t.\tG\t.\t1748\tPASS\tDP=45;TD=87;BQ=39;MQ=49;QD=38;BC=0,0,45,0;QP=0,0,100,0;PC=56;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t11\t.\tA\t.\t2104\tPASS\tDP=55;TD=104;BQ=38;MQ=51;QD=38;BC=55,0,0,0;QP=100,0,0,0;PC=58;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t12\t.\tC\t.\t2222\tPASS\tDP=56;TD=106;BQ=40;MQ=51;QD=39;BC=0,56,0,0;QP=0,100,0,0;PC=59;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t13\t.\tC\t.\t2231\tPASS\tDP=56;TD=106;BQ=40;MQ=51;QD=39;BC=0,56,0,0;QP=0,100,0,0;PC=59;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t14\t.\tC\t.\t2237\tPASS\tDP=56;TD=107;BQ=40;MQ=51;QD=39;BC=0,56,0,0;QP=0,100,0,0;PC=59;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t15\t.\tC\t.\t2230\tPASS\tDP=56;TD=107;BQ=40;MQ=51;QD=39;BC=0,56,0,0;QP=0,100,0,0;PC=60;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t16\t.\tG\t.\t2236\tPASS\tDP=56;TD=107;BQ=40;MQ=51;QD=39;BC=0,0,56,0;QP=0,0,100,0;PC=61;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t17\t.\tG\t.\t2213\tPASS\tDP=56;TD=108;BQ=40;MQ=51;QD=39;BC=0,0,56,0;QP=0,0,100,0;PC=64;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t18\t.\tT\t.\t2178\tPASS\tDP=56;TD=108;BQ=39;MQ=51;QD=38;BC=0,0,0,56;QP=0,0,0,100;PC=65;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t19\t.\tT\t.\t2161\tPASS\tDP=56;TD=110;BQ=39;MQ=51;QD=38;BC=0,0,0,56;QP=0,0,0,100;PC=66;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t20\t.\tC\t.\t2164\tPASS\tDP=56;TD=110;BQ=39;MQ=51;QD=38;BC=0,56,0,0;QP=0,100,0,0;PC=70;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t21\t.\tA\t.\t2188\tPASS\tDP=57;TD=112;BQ=38;MQ=51;QD=38;BC=57,0,0,0;QP=100,0,0,0;PC=72;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t22\t.\tG\t.\t2127\tPASS\tDP=56;TD=112;BQ=38;MQ=51;QD=37;BC=0,0,56,0;QP=0,0,100,0;PC=72;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t23\t.\tG\t.\t2102\tPASS\tDP=55;TD=112;BQ=38;MQ=51;QD=38;BC=0,0,55,0;QP=0,0,100,0;PC=73;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t24\t.\tC\t.\t2082\tPASS\tDP=55;TD=113;BQ=38;MQ=51;QD=37;BC=0,55,0,0;QP=0,100,0,0;PC=74;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t25\t.\tT\t.\t2138\tPASS\tDP=56;TD=111;BQ=38;MQ=51;QD=38;BC=0,0,0,56;QP=0,0,0,100;PC=74;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t26\t.\tT\t.\t2126\tPASS\tDP=55;TD=112;BQ=39;MQ=51;QD=38;BC=0,0,0,55;QP=0,0,0,100;PC=75;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t27\t.\tC\t.\t2193\tPASS\tDP=58;TD=115;BQ=38;MQ=51;QD=37;BC=0,58,0,0;QP=0,100,0,0;PC=75;IC=0;DC=0;XC='..b'=100,0,0,0;PC=89;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t58\t.\tC\t.\t1542\tPASS\tDP=47;TD=101;BQ=33;MQ=57;QD=32;BC=0,47,0,0;QP=0,100,0,0;PC=89;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t59\t.\tT\t.\t1656\tPASS\tDP=48;TD=102;BQ=35;MQ=57;QD=34;BC=0,0,0,48;QP=0,0,0,100;PC=90;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t60\t.\tT\t.\t1610\tPASS\tDP=45;TD=99;BQ=36;MQ=57;QD=35;BC=0,0,0,45;QP=0,0,0,100;PC=90;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t61\t.\tA\t.\t1494\tPASS\tDP=43;TD=96;BQ=35;MQ=57;QD=34;BC=43,0,0,0;QP=100,0,0,0;PC=91;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t62\t.\tA\t.\t1479\tPASS\tDP=43;TD=95;BQ=34;MQ=57;QD=34;BC=43,0,0,0;QP=100,0,0,0;PC=91;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t63\t.\tC\t.\t1569\tPASS\tDP=45;TD=96;BQ=35;MQ=58;QD=34;BC=0,45,0,0;QP=0,100,0,0;PC=91;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t64\t.\tG\t.\t1519\tPASS\tDP=44;TD=95;BQ=35;MQ=58;QD=34;BC=0,0,44,0;QP=0,0,100,0;PC=91;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t65\t.\tG\t.\t1472\tPASS\tDP=43;TD=92;BQ=34;MQ=58;QD=34;BC=0,0,43,0;QP=0,0,100,0;PC=91;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t66\t.\tC\t.\t1336\tPASS\tDP=40;TD=91;BQ=33;MQ=59;QD=33;BC=0,40,0,0;QP=0,100,0,0;PC=91;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t67\t.\tG\t.\t1338\tPASS\tDP=40;TD=91;BQ=33;MQ=59;QD=33;BC=0,0,40,0;QP=0,0,100,0;PC=91;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t68\t.\tA\t.\t1232\tPASS\tDP=38;TD=87;BQ=32;MQ=59;QD=32;BC=38,0,0,0;QP=100,0,0,0;PC=92;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t69\t.\tC\t.\t1192\tPASS\tDP=35;TD=86;BQ=34;MQ=59;QD=34;BC=0,35,0,0;QP=0,100,0,0;PC=93;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t70\t.\tC\t.\t1115\tPASS\tDP=32;TD=81;BQ=35;MQ=59;QD=34;BC=0,32,0,0;QP=0,100,0,0;PC=93;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t71\t.\tC\t.\t1093\tPASS\tDP=31;TD=84;BQ=35;MQ=60;QD=35;BC=0,31,0,0;QP=0,100,0,0;PC=93;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t72\t.\tT\t.\t1055\tPASS\tDP=30;TD=80;BQ=35;MQ=60;QD=35;BC=0,0,0,30;QP=0,0,0,100;PC=94;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t73\t.\tA\t.\t1016\tPASS\tDP=29;TD=80;BQ=35;MQ=60;QD=35;BC=29,0,0,0;QP=100,0,0,0;PC=99;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t74\t.\tA\t.\t994\tPASS\tDP=29;TD=80;BQ=34;MQ=60;QD=34;BC=29,0,0,0;QP=100,0,0,0;PC=100;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t75\t.\tG\t.\t1023\tPASS\tDP=29;TD=81;BQ=35;MQ=60;QD=35;BC=0,0,29,0;QP=0,0,100,0;PC=102;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t76\t.\tG\t.\t996\tPASS\tDP=28;TD=80;BQ=36;MQ=60;QD=35;BC=0,0,28,0;QP=0,0,100,0;PC=104;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t77\t.\tT\t.\t919\tPASS\tDP=26;TD=79;BQ=35;MQ=60;QD=35;BC=0,0,0,26;QP=0,0,0,100;PC=104;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t78\t.\tT\t.\t912\tPASS\tDP=26;TD=79;BQ=35;MQ=60;QD=35;BC=0,0,0,26;QP=0,0,0,100;PC=104;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t79\t.\tG\t.\t832\tPASS\tDP=25;TD=78;BQ=33;MQ=60;QD=33;BC=0,0,25,0;QP=0,0,100,0;PC=104;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t80\t.\tA\t.\t788\tPASS\tDP=23;TD=77;BQ=34;MQ=60;QD=34;BC=23,0,0,0;QP=100,0,0,0;PC=104;IC=0;DC=0;XC=1;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t81\t.\tC\t.\t803\tPASS\tDP=23;TD=75;BQ=35;MQ=60;QD=34;BC=0,23,0,0;QP=0,100,0,0;PC=104;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t82\t.\tG\t.\t807\tPASS\tDP=24;TD=75;BQ=34;MQ=60;QD=33;BC=0,0,24,0;QP=0,0,100,0;PC=104;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t83\t.\tA\t.\t1025\tPASS\tDP=29;TD=82;BQ=35;MQ=60;QD=35;BC=29,0,0,0;QP=100,0,0,0;PC=106;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n+gi|448814763|ref|NC_000962.3|\t84\t.\tC\t.\t1080\tPASS\tDP=30;TD=84;BQ=36;MQ=60;QD=36;BC=0,30,0,0;QP=0,100,0,0;PC=106;IC=0;DC=0;XC=0;AC=0;AF=0.00\tGT\t0/0\n' |
| b |
| diff -r 000000000000 -r fe0dc27e6327 test-data/test1.bam |
| b |
| Binary file test-data/test1.bam has changed |
| b |
| diff -r 000000000000 -r fe0dc27e6327 test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fasta Sat Aug 13 04:50:55 2016 -0400 |
| b |
| b'@@ -0,0 +1,168 @@\n+>gi|448814763|ref|NC_000962.3| NC_000962.3 Mycobacterium tuberculosis H37Rv, complete genome\n+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT\n+AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG\n+ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT\n+GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC\n+CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC\n+GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT\n+ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG\n+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC\n+GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC\n+GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT\n+TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG\n+GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG\n+GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC\n+AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG\n+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC\n+GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC\n+CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC\n+ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC\n+ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC\n+GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC\n+GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC\n+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG\n+GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC\n+AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC\n+CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC\n+ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC\n+TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC\n+CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG\n+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC\n+TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT\n+TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAA\n+CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC\n+TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCATTC\n+GTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTCATCGTGAGGT\n+GAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT\n+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGC\n+CCGCGGTGCCGGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTT\n+CCGGATTCGACTACGAGGTTTCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTG\n+GAAGCGTTTTAGTTTCTGGCCGATTGTTGTCCGATATTACCCGGGCGTTGCCTAACAAGC\n+CCGTAGACGTTCATGTCGAAGGTAACCGGGTCGCATTGACCTGCGGTAACGCCAGGTTTT\n+CGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCGGAAGAGACCG\n+GATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC\n+GGGACGACACGTTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGG\n+TTTTGGCCGCTACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGT\n+CGCCAGATATCGAAGCGGCTGTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAG\n+CGGGCATCGGCGGCTCTGACGTTCGTTTGTCGTTGGGTACTGGGCCGGGGGTGGGCAAGG\n+ATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCACCACGCGACTTCTTGATGCCG\n+AGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCCACCATGGACG\n+TGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG\n+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGAC\n+GAGCCGAGGAAGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACC\n+CAACCTATCTAACGGACGGTTTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTA\n+CGACTGCGGGTAAGCCTGCCTTGCTACGTCCGGTGTCCGGGGACGATCGCCCTGTGGCGG\n+GTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGACTATGTCTATCTGTTGATGC\n+CGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCGTCATTTGGGG\n+CTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT\n+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACG\n+ACGTTAGGTTCGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGT\n+GCGGTGATCTCCACGATCGTGGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATC\n+GCCACGGGGCGAGTCAACAAAGCGCGATTGAATCGATCATCGGTCCGAAGTACACGTGAT\n+GTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGGATCTGGGGTTGGTTCGTGGG\n+GATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAGGCCTGCGATC\n+GCTGCGGTACGAGCCGAATATGAGAGGGTGTTGCGCCAGCGG'..b'TCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGG\n+CACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGA\n+CCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT\n+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAA\n+GTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCA\n+CTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGC\n+GCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGA\n+CATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGA\n+ACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGAT\n+GTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA\n+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCA\n+CGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGA\n+TGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCC\n+GCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCA\n+GCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGG\n+GCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGG\n+TGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCG\n+TCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGA\n+GGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGA\n+TGTCTAACGCAACCCTGCGTTCGATTGCAAACGAGGAATAGATGACAGACACGACGTTGC\n+CGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCGAGCAGGAGATGCAGCGCA\n+GCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACG\n+GGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGG\n+ACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGC\n+ACGGCGACGCGTCGATCTACGACAGCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCT\n+ACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGA\n+TGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACG\n+AGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTAC\n+CCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAA\n+CCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGA\n+ATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGG\n+ACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTG\n+GCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTA\n+CCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGA\n+TCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTA\n+GCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGG\n+TGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAG\n+CGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTG\n+ACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGC\n+GAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCAC\n+TGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACA\n+TCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGG\n+AACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAG\n+ACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCG\n+TGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCG\n+ACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCA\n+AGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTG\n+CGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGA\n+TCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGG\n+CCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAAC\n+GCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCA\n+CTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCG\n+GAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGG\n+CCGGCGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCG\n+ACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATA\n+TCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGA\n+CGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCG\n+GTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGA\n+TTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCG\n+CGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGG\n+GCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATG\n+CCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAATCAGGCTCGCCCGACGACGATG\n+CGGATCGCGTAGCGATCTGAGGAGGAATCGGGCAGCTAGGCTCGGCAGCCGGGTACGAGT\n+GTTAGGAGTCGGGGTGACTGCACCGAACGAGCCGGGGGCGCTCAGCAAGGGCGACGGCCC\n+GAATGCGGATGGCTTGGTCGACCGTGGGGGCGCACATCGG\n' |
| b |
| diff -r 000000000000 -r fe0dc27e6327 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Aug 13 04:50:55 2016 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> + |