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epic2/.shed.yml epic2/epic2_wrapper.xml epic2/macros.xml epic2/test-data/control.bam epic2/test-data/control.bed.gz epic2/test-data/epic2_results.txt epic2/test-data/epic2_results1.txt epic2/test-data/epic2_results2.txt epic2/test-data/epic2_results3.bed epic2/test-data/epic2_results3.txt epic2/test-data/test.bam epic2/test-data/test.bed.gz epic2/test-data/test_ChIP.bam epic2/test-data/test_Input.bam epic2/test-data/test_chromsizes.txt epic2/test-data/test_fasta.fasta epic2/tool-data/fasta_indexes.loc.sample epic2/tool_data_table_conf.xml.sample |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/.shed.yml Wed May 08 08:30:21 2019 -0400 |
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| @@ -0,0 +1,6 @@ +categories: [ChIP-seq] +description: Peak calling of broad ChIP-Seq marks +homepage_url: https://github.com/biocore-ntnu/epic2 +name: epic2 +owner: mpaya +remote_repository_url: https://github.com/wilkinsonlab/galaxy_tools/epic2/ \ No newline at end of file |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/epic2_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/epic2_wrapper.xml Wed May 08 08:30:21 2019 -0400 |
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| b'@@ -0,0 +1,372 @@\n+<tool id="epic2" name="epic2" version="@VERSION@.0">\n+ <description>peak calling of broad ChIP-Seq marks</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ \n+ <stdio>\n+ <exit_code range="1:125" level="fatal" description="Unknown error occurred" />\n+ <exit_code range="130:" level="fatal" description="Unknown error occurred" />\n+ <regex match="epic2: (command ){0,1}not found" source="stderr" level="fatal" description="The epic2 python package is not properly installed, contact Galaxy administrators" />\n+ </stdio>\n+ \n+ <command><![CDATA[\n+\n+ ##set up treatment files, extension must be bed, bedpe, bam, sam\n+ #set $t_file_list = list()\n+ #if str($treatment.t_multi_select) == "No":\n+ #if $treatment.input_treatment_file.is_of_type(\'bed\')\n+ #set $t_file = \'ChIP_file.bed\'\n+ ln -s \'$treatment.input_treatment_file\' $t_file &&\n+ #elif $treatment.input_treatment_file.is_of_type(\'bam\')\n+ #set $t_file = \'ChIP_file.bam\'\n+ ln -s \'$treatment.input_treatment_file\' $t_file &&\n+ ln -s \'$treatment.input_treatment_file.metadata.bam_index\' ${t_file}.bai &&\n+ #elif $treatment.input_treatment_file.is_of_type(\'sam\')\n+ #set $t_file = \'ChIP_file.sam\'\n+ ln -s \'$treatment.input_treatment_file\' $t_file &&\n+ #end if\n+ $t_file_list.append($t_file)\n+ #else\n+ #set $inputs = $treatment.input_treatment_file\n+ #for $i, $f in enumerate($inputs)\n+ #if $f.is_of_type(\'bed\')\n+ #set $t_file = \'\'.join([\'ChIP_file_\',str($i),\'.bed\'])\n+ ln -s \'$f\' $t_file &&\n+ #elif $f.is_of_type(\'bam\')\n+ #set $t_file = \'\'.join([\'ChIP_file_\',str($i),\'.bam\'])\n+ ln -s \'$f\' $t_file &&\n+ ln -s \'$f.metadata.bam_index\' ${t_file}.bai &&\n+ #elif $f.is_of_type(\'sam\')\n+ #set $t_file = \'\'.join([\'ChIP_file_\',str($i),\'.sam\'])\n+ ln -s \'$f\' $t_file &&\n+ #end if\n+ $t_file_list.append($t_file)\n+ #end for\n+ #end if\n+\n+ ##set up control files, extension must be bed, bedpe, bam, sam\n+ #if str($control.c_select) == "Yes":\n+ #set $c_file_list = list()\n+ #if str($control.c_multiple.c_multi_select) == "No":\n+ #set $f = $control.c_multiple.input_control_file\n+ #if $f.is_of_type(\'bed\')\n+ #set $c_file = \'control_file.bed\'\n+ ln -s \'$f\' $c_file &&\n+ #elif $f.is_of_type(\'bam\')\n+ #set $c_file = \'control_file.bam\'\n+ ln -s \'$f\' $c_file &&\n+ ln -s \'$f.metadata.bam_index\' ${c_file}.bai &&\n+ #elif $f.is_of_type(\'sam\')\n+ #set $c_file = \'control_file.sam\'\n+ ln -s \'$f\' $c_file &&\n+ #end if\n+ $c_file_list.append($c_file)\n+ #else\n+ #set $inputs = $control.c_multiple.input_control_file\n+ #for $i, $f in enumerate($inputs)\n+ #if $f.is_of_type(\'bed\')\n+ #set $c_file = \'\'.join([\'control_file\',str($i),\'.bed\'])\n+ ln -s \'$f\' $c_file &&\n+ #elif $f.is_of_type(\'bam\')\n+ #set $c_file = \'\'.join([\'control_file\',str($i),\'.bam\'])\n+ ln -s \'$f\' $c_file &&\n+ ln -s \'$f.metadata.bam_index\' ${c_file}.bai &&\n+ #elif $f.is_of_type(\'sam\')\n+ #set $c_file = \'\'.join([\'control_file\',str($i),\'.sam\'])\n+ ln -s \'$f\' $c_file &&\n+ #end if\n+ $c_file_list.append($c_file)\n+ '..b'" type="integer" optional="True" label="Fragment size" \n+ help="(Single end reads only) Size of the sequenced fragment. Each read is extended half the fragment size from the 5\' end. \n+ Default 150 (i.e. extend by 75). (--fragment-size)" />\n+ <param name="original_algorithm" type="boolean" checked="false" truevalue="--original-algorithm" falsevalue="" \n+ label="Compute p-values with SICER original algorithm?" \n+ help="Use the original SICER algorithm, without the epic2 fix. This will use all reads in your files to compute\n+ the p-values, including those falling outside the genome boundaries. (--original-algorithm)" />\n+ </section>\n+ </inputs>\n+\n+ <outputs>\n+ <data format="tabular" name="peaks" label="${tool.name} on ${on_string}"/>\n+ <data format=\'bed\' name=\'bed_peaks\' label="${tool.name} on ${on_string}: BED">\n+ <filter>to_bed</filter>\n+ </data>\n+\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="input_treatment_file" value="test.bam" ftype="bam" />\n+ <param name="c_select" value="Yes" />\n+ <param name="input_control_file" value="control.bam" ftype="bam"/>\n+ <output name="peaks" file="epic2_results.txt"/>\n+ </test>\n+ <test>\n+ <param name="input_treatment_file" value="test.bed.gz" ftype="bed" />\n+ <param name="c_select" value="Yes" />\n+ <param name="input_control_file" value="control.bed.gz" ftype="bed"/>\n+ <output name="peaks" file="epic2_results1.txt"/>\n+ </test>\n+ <test>\n+ <param name="input_treatment_file" value="test_ChIP.bam" ftype="bam" />\n+ <param name="c_select" value="Yes" />\n+ <param name="input_control_file" value="test_Input.bam" ftype="bam"/>\n+ <param name="g_select" value="No" />\n+ <param name="chr_select" value="No" />\n+ <param name="cs_file" value="test_chromsizes.txt" />\n+ <param name="egf" value="0.99" />\n+ <param name="original_algorithm" value="Yes" />\n+ <output name="peaks" file="epic2_results2.txt"/>\n+ </test>\n+ <test>\n+ <param name="input_treatment_file" value="test_ChIP.bam" ftype="bam" />\n+ <param name="c_select" value="Yes" />\n+ <param name="input_control_file" value="test_Input.bam" ftype="bam"/>\n+ <param name="g_select" value="No" />\n+ <param name="chr_select" value="No" />\n+ <param name="cs_file" value="test_fasta.fasta" />\n+ <param name="egf" value="0.99" />\n+ <param name="to_bed" value="Yes" />\n+ <param name="mapq" value="10" />\n+ <param name="bin_size" value="100" />\n+ <param name="gaps_allowed" value="0" />\n+ <output name="peaks" file="epic2_results3.txt"/>\n+ <output name="bed_peaks" file="epic2_results3.bed"/>\n+ </test>\n+ </tests>\n+\n+ <help>\n+Chip-Seq broad peak/domain finder based on SICER.\n+\n+**Accepted input formats**\n+\n+Input file extension must be bed, bedpe, bam or sam.\n+\n+**Broad peaks format**\n+ \n+Original epic2 output does not follow any standard format, then broad peaks bed format is offered. This format follows the standard from ENCODE, BED 6 + 3, and contains the following columns:\n+ \n+ * **1.** Chrom \n+ * **2.** Start \n+ * **3.** End \n+ * **4.** Name \n+ * **5.** Score \n+ * **6.** Strand \n+ * **7.** log2FoldChange \n+ * **8.** -log10PValue \n+ * **9.** -log10FDR\n+ \n+.. class:: warningmark\n+\n+ On columns 8 and 9, the max value is set to 50 when Pvalue == 0.0.\n+\n+Tool adapted to Galaxy by Miriam Pay\xc3\xa1 Milans. Original documentation on https://github.com/biocore-ntnu/epic2.\n+ \n+ \n+ </help>\n+ <expand macro="citations" />\n+</tool> \n' |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/macros.xml Wed May 08 08:30:21 2019 -0400 |
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| @@ -0,0 +1,117 @@ +<macros> + + <token name="@VERSION@">1.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.26">epic2</requirement> + <requirement type="package">htslib</requirement> + </requirements> + </xml> + + <xml name="effectiveGenomeSize"> + <param name="builtin_genome" argument="--genome" type="select" label="Genome" help="Default hg19 (--genome)" > + <option value="ailMel1">ailMel1</option> + <option value="anoCar2">anoCar2</option> + <option value="apiMel1">apiMel1</option> + <option value="aplCal1">aplCal1</option> + <option value="aquChr2">aquChr2</option> + <option value="balAcu1">balAcu1</option> + <option value="braFlo1">braFlo1</option> + <option value="calJac1">calJac1</option> + <option value="calJac3">calJac3</option> + <option value="cavPor3">cavPor3</option> + <option value="ce10">ce10</option> + <option value="ce11">ce11</option> + <option value="cerSim1">cerSim1</option> + <option value="chlSab2">chlSab2</option> + <option value="chrPic1">chrPic1</option> + <option value="danRer10">danRer10</option> + <option value="danRer3">danRer3</option> + <option value="danRer4">danRer4</option> + <option value="danRer5">danRer5</option> + <option value="danRer6">danRer6</option> + <option value="danRer7">danRer7</option> + <option value="dm3">dm3</option> + <option value="dm6">dm6</option> + <option value="echTel2">echTel2</option> + <option value="equCab1">equCab1</option> + <option value="equCab2">equCab2</option> + <option value="eriEur1">eriEur1</option> + <option value="eriEur2">eriEur2</option> + <option value="fr1">fr1</option> + <option value="fr2">fr2</option> + <option value="galVar1">galVar1</option> + <option value="gasAcu1">gasAcu1</option> + <option value="geoFor1">geoFor1</option> + <option value="gorGor3">gorGor3</option> + <option value="gorGor4">gorGor4</option> + <option value="gorGor5">gorGor5</option> + <option value="hetGla1">hetGla1</option> + <option value="hetGla2">hetGla2</option> + <option value="hg18">hg18</option> + <option value="hg19" selected="true">hg19</option> + <option value="hg38">hg38</option> + <option value="loxAfr3">loxAfr3</option> + <option value="macEug2">macEug2</option> + <option value="melGal1">melGal1</option> + <option value="melGal5">melGal5</option> + <option value="micMur2">micMur2</option> + <option value="mm10">mm10</option> + <option value="mm9">mm9</option> + <option value="monDom4">monDom4</option> + <option value="monDom5">monDom5</option> + <option value="myoLuc2">myoLuc2</option> + <option value="nanPar1">nanPar1</option> + <option value="nasLar1">nasLar1</option> + <option value="nomLeu1">nomLeu1</option> + <option value="nomLeu2">nomLeu2</option> + <option value="nomLeu3">nomLeu3</option> + <option value="ochPri3">ochPri3</option> + <option value="oreNil2">oreNil2</option> + <option value="ornAna1">ornAna1</option> + <option value="ornAna2">ornAna2</option> + <option value="oryCun2">oryCun2</option> + <option value="oryLat2">oryLat2</option> + <option value="oviAri1">oviAri1</option> + <option value="oviAri3">oviAri3</option> + <option value="papAnu2">papAnu2</option> + <option value="petMar1">petMar1</option> + <option value="petMar2">petMar2</option> + <option value="ponAbe2">ponAbe2</option> + <option value="priPac1">priPac1</option> + <option value="rheMac2">rheMac2</option> + <option value="rheMac3">rheMac3</option> + <option value="rheMac8">rheMac8</option> + <option value="rhiRox1">rhiRox1</option> + <option value="rn4">rn4</option> + <option value="rn5">rn5</option> + <option value="rn6">rn6</option> + <option value="sacCer1">sacCer1</option> + <option value="sacCer2">sacCer2</option> + <option value="sacCer3">sacCer3</option> + <option value="saiBol1">saiBol1</option> + <option value="sorAra2">sorAra2</option> + <option value="speTri2">speTri2</option> + <option value="strPur1">strPur1</option> + <option value="strPur2">strPur2</option> + <option value="susScr2">susScr2</option> + <option value="susScr3">susScr3</option> + <option value="taeGut1">taeGut1</option> + <option value="taeGut2">taeGut2</option> + <option value="tarSyr2">tarSyr2</option> + <option value="tetNig1">tetNig1</option> + <option value="tetNig2">tetNig2</option> + <option value="triMan1">triMan1</option> + <option value="xenTro3">xenTro3</option> + <option value="xenTro7">xenTro7</option> + </param> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">0.1093/bioinformatics/btz232</citation> + <yield /> + </citations> + </xml> + +</macros> |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/control.bam |
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| Binary file epic2/test-data/control.bam has changed |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/control.bed.gz |
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| Binary file epic2/test-data/control.bed.gz has changed |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/epic2_results.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/test-data/epic2_results.txt Wed May 08 08:30:21 2019 -0400 |
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| b'@@ -0,0 +1,166 @@\n+#Chromosome\tStart\tEnd\tPValue\tScore\tStrand\tChIPCount\tInputCount\tFDR\tlog2FoldChange\n+chr1\t23568400\t23568599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t26401200\t26401399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t33054800\t33055399\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr1\t33365200\t33365399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t39422200\t39422799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr1\t51473600\t51474399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr1\t58785200\t58786199\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr1\t59430000\t59430199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t65065600\t65066199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr1\t91625400\t91625799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr1\t100589600\t100589799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t103840400\t103841199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr1\t113416400\t113416799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr1\t113486600\t113487199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr1\t115014800\t115014999\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t144181600\t144181999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr1\t171053400\t171054599\t2.0859275044291852e-11\t930.748585550573\t.\t3\t0\t6.925279314704895e-10\t9.30748585550573\n+chr1\t181707400\t181707999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr1\t203357400\t203357799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr1\t210178400\t210178999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr1\t210471400\t210471599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t219659800\t219660199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr1\t220704400\t220705199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t32400\t33399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr2\t15618800\t15619599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t39208000\t39208799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t48521000\t48521199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr2\t61986000\t61986599\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr2\t73314400\t73315199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t101681600\t101682399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t136216000\t136216799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t175474200\t175474599\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr2\t181811200\t181811799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr2\t201039600\t201040199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr2\t202215400\t202215799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr2\t207865600\t207866599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr2\t224033800\t224034799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.98555776'..b'.30748585550573\n+chr13\t113095600\t113095999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr14\t30160600\t30161599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr14\t44201400\t44201799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr14\t54727600\t54727799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr14\t67356600\t67356999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr14\t75051400\t75051799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr14\t76404200\t76404399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr14\t76912200\t76912799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr15\t38781800\t38782599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr15\t57638400\t57638999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr15\t76517200\t76517399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr16\t9080000\t9080599\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr16\t20683000\t20683799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t20724800\t20725799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr16\t22216800\t22217199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr16\t28892800\t28893599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t30612600\t30612999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr16\t52910600\t52911399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t65955600\t65956399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t67987600\t67988199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr16\t83646600\t83647399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t83749000\t83749599\t1.306175776413088e-12\t1000.0\t.\t3\t0\t7.227505962819087e-11\t10.30748585550573\n+chr17\t6340000\t6340199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr17\t8036400\t8036799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr17\t16496800\t16497799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr17\t30567400\t30568399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr17\t34235000\t34235399\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr17\t35277000\t35277399\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chr17\t71748600\t71748799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr18\t9324200\t9324399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr18\t14914400\t14915399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr19\t17239200\t17239799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr19\t45288400\t45288999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n+chr20\t43477600\t43477799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr22\t16398800\t16399599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr22\t35502000\t35502999\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chrX\t37591800\t37592199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n+chrX\t76940200\t76940599\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n' |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/epic2_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/test-data/epic2_results1.txt Wed May 08 08:30:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,166 @@\n+#Chromosome\tStart\tEnd\tPValue\tScore\tStrand\tChIPCount\tInputCount\tFDR\tlog2FoldChange\n+chr1\t23568400\t23568599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t26401200\t26401399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t33054800\t33055399\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr1\t33365200\t33365399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t39422200\t39422799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr1\t51473600\t51474399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr1\t58785200\t58786199\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr1\t59430000\t59430199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t65065600\t65066199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr1\t91625400\t91625799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr1\t100589600\t100589799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t103840400\t103841199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr1\t113416400\t113416799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr1\t113486600\t113487199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr1\t115014800\t115014999\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t144181400\t144181999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr1\t171053400\t171054599\t2.0859275044291852e-11\t930.748585550573\t.\t3\t0\t6.925279314704895e-10\t9.30748585550573\n+chr1\t181707400\t181707999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr1\t203357400\t203357799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr1\t210178400\t210178999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr1\t210471400\t210471599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr1\t219659800\t219660199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr1\t220704400\t220705199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t32400\t33399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr2\t15618800\t15619599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t39208000\t39208799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t48521000\t48521199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr2\t61986000\t61986599\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr2\t73314400\t73315199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t101681600\t101682399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t136216000\t136216799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr2\t175474200\t175474599\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr2\t181811200\t181811799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr2\t201039600\t201040199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr2\t202215400\t202215799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr2\t207865600\t207866599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr2\t224033800\t224034799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8'..b'.30748585550573\n+chr13\t113095600\t113095999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr14\t30160600\t30161599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr14\t44201400\t44201799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr14\t54727600\t54727799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr14\t67356600\t67356999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr14\t75051400\t75051799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr14\t76404200\t76404399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr14\t76912200\t76912799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr15\t38781800\t38782599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr15\t57638400\t57638999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr15\t76517200\t76517399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr16\t9080000\t9080599\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr16\t20683000\t20683799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t20724800\t20725799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr16\t22216800\t22217199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr16\t28892800\t28893599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t30612600\t30612999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr16\t52910600\t52911399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t65955600\t65956399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t67987600\t67988199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr16\t83646600\t83647399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr16\t83749000\t83749599\t1.306175776413088e-12\t1000.0\t.\t3\t0\t7.227505962819087e-11\t10.30748585550573\n+chr17\t6340000\t6340199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr17\t8036400\t8036799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr17\t16496800\t16497799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr17\t30567400\t30568399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr17\t34235000\t34235399\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr17\t35277000\t35277399\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chr17\t71748600\t71748799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr18\t9324200\t9324399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr18\t14914400\t14915399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chr19\t17239200\t17239799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr19\t45288400\t45288999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n+chr20\t43477600\t43477799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n+chr22\t16398800\t16399599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n+chr22\t35502000\t35502999\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n+chrX\t37591800\t37592199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n+chrX\t76940200\t76940599\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n' |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/epic2_results2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/test-data/epic2_results2.txt Wed May 08 08:30:21 2019 -0400 |
| b |
| @@ -0,0 +1,10 @@ +#Chromosome Start End PValue Score Strand ChIPCount InputCount FDR log2FoldChange +chr4 17800 18799 3.111675555106485e-25 129.5809069871083 . 172 59 4.445250793009265e-25 1.2958090698710831 +chr4 32000 33799 7.8685062790203735e-115 197.92562730767474 . 412 88 1.5737012558040745e-114 1.9792562730767476 +chr4 41600 46999 7.479314004730516e-245 168.2151595038671 . 1166 306 7.479314004730516e-244 1.6821515950386712 +chr4 61800 66399 1.4988860864785783e-165 152.4906706437191 . 926 271 7.494430432392892e-165 1.524906706437191 +chr4 72800 77799 4.26634983112049e-134 146.53062167426648 . 800 244 1.0665874577801224e-133 1.465306216742665 +chr4 78600 78999 5.6625739181345514e-05 103.22952837235616 . 34 14 6.29174879792728e-05 1.0322952837235615 +chr4 80600 81599 2.777975572732711e-17 103.59803305314176 . 168 69 3.472469465915889e-17 1.0359803305314177 +chr4 85600 87399 2.6091166307239775e-59 143.26724762962738 . 359 112 4.348527717873296e-59 1.4326724762962737 +chr4 89600 92199 3.3232371576770455e-142 174.76146347410025 . 630 158 1.1077457192256818e-141 1.7476146347410024 |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/epic2_results3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/test-data/epic2_results3.bed Wed May 08 08:30:21 2019 -0400 |
| b |
| @@ -0,0 +1,11 @@ +chr4 17800 18699 island_1 136 . 1.367561922471873 25.8998 25.6309 +chr4 32100 33699 island_2 232 . 2.32156573905299 142.531 141.894 +chr4 41500 46999 island_3 167 . 1.6743920068364044 244.104 242.99 +chr4 55500 55599 island_4 74 . 0.7474099932884168 1.38871 1.31616 +chr4 60900 60999 island_5 74 . 0.7474099932884168 1.50708 1.39314 +chr4 61900 66399 island_6 155 . 1.550841347409922 168.128 167.315 +chr4 72700 77899 island_7 143 . 1.43860868673979 131.985 131.57 +chr4 78600 78899 island_8 127 . 1.2779247099871966 4.67152 4.51182 +chr4 80600 81599 island_9 103 . 1.031202959289008 16.4299 16.2191 +chr4 85600 87299 island_10 146 . 1.4694673801584501 60.1299 59.7941 +chr4 89000 92299 island_11 163 . 1.6325895912865587 135.464 134.952 |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/epic2_results3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/test-data/epic2_results3.txt Wed May 08 08:30:21 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ +#Chromosome Start End PValue Score Strand ChIPCount InputCount FDR log2FoldChange +chr4 17800 18699 1.2596293166425706e-26 136.7561922471873 . 166 54 2.339311588050488e-26 1.367561922471873 +chr4 32100 33699 2.946445596867846e-143 232.156573905299 . 399 67 1.2767930919760667e-142 2.32156573905299 +chr4 41500 46999 7.868596428937404e-245 167.43920068364045 . 1175 309 1.0229175357618626e-243 1.6743920068364044 +chr4 55500 55599 0.0408590134545058 74.74099932884168 . 10 5 0.04828792499168868 0.7474099932884168 +chr4 60900 60999 0.031111272762994507 74.74099932884168 . 12 6 0.04044465459189286 0.7474099932884168 +chr4 61900 66399 7.454733262747862e-169 155.0841347409922 . 918 263 4.84557662078611e-168 1.550841347409922 +chr4 72700 77899 1.0341241230257782e-132 143.860868673979 . 817 253 2.6887227198670233e-132 1.43860868673979 +chr4 78600 78899 2.1304915144814984e-05 127.79247099871966 . 26 9 3.077376632028831e-05 1.2779247099871966 +chr4 80600 81599 3.715910533402511e-17 103.1202959289008 . 168 69 6.03835461677908e-17 1.031202959289008 +chr4 85600 87299 7.414135910777427e-61 146.946738015845 . 353 107 1.6063961140017758e-60 1.4694673801584501 +chr4 89000 92299 3.4369281602401456e-136 163.25895912865587 . 676 183 1.1170016520780473e-135 1.6325895912865587 |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/test.bam |
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| Binary file epic2/test-data/test.bam has changed |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/test.bed.gz |
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| Binary file epic2/test-data/test.bed.gz has changed |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/test_ChIP.bam |
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| Binary file epic2/test-data/test_ChIP.bam has changed |
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| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/test_Input.bam |
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| Binary file epic2/test-data/test_Input.bam has changed |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/test_chromsizes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/test-data/test_chromsizes.txt Wed May 08 08:30:21 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chr4 99999 |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/test-data/test_fasta.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/test-data/test_fasta.fasta Wed May 08 08:30:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,1001 @@\n+>chr4\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG\n+GACAGCGGAATCCTCGACCCGGTTGAGGAATGGTCGACGAAAATCTATCGGGTTCGAGGATTCGTCGACCAGGTGTTGGAATCGTCGACCGAGTCTGAGA\n+ATTCGTAGACCAGGACGGCGGAATCCTCGACAATGACGAGGTATGGTCGAGGAAAATCTATCGGGTTCGAGGATTCGTCTACCAGGTGATGGAATCCTCG\n+ACCAGGACAAAGAATTCGTCGACCAGGGGTGGAATTGTTGTTATTCCGATCATGAGAGCGGATATCAGTACAGATCCGACGCTGGTGAAAAAGATCACGG\n+CGATCGTGGATAGTATCAAGCCACCGAGAGTCTCGTATTCGGAGAAAGATCGGCCGATGAGGATAAGAGGTCGATCGGATGGACGGAAGAGGTAGAGGAA\n+GAGCCATGAAGCGGCGAGGCATAGGAGGAGGATGAGCGAGAATGGGTGGGCGGGAAGAGAGAAACTGATGATCAGAGCGATGATGCAGACGTAATTCACC\n+CTGAAATAAGAGGAGTTCTTCCAGAATCGCGTCATGGCCTCGAAGACAGAGTCAAGCTTGGTGAAAAGCAGATCGTTCGAGGAGCTCTGACCACGGCCGG\n+CTACGAGATAGACCACCACGAACCGTCTTGGTCACACTGTTGACAAATGCATGGACGGTTGGAGGTTGTGATTCCACCACATCAGTTACAATCGGAGGCT\n+GATCCGGACTTGGCTGTTGCGGTGGTGGAAATCGGAAGCACAGGGGGATTTGTGGACACCATTCGATTTTGTTCTTTAGGGATTTCAAGATTGGAAAATT\n+TTAGGAGACGATTGATTTGGAAGTCGGTGAAGTTTCGGTAGTGTTATGTATTTATTTTTTTTGTCATAAGCGGTAGCGTTATGTATTTGTAAGATCACAT\n+TAAGCGTCTTTCAACTTTGATTATACGCATTGCTTCATCTGATATCTAATCCATATTTTGATCAAAGTGACATTTGATAAAATAAAATAAAACTAACCTA\n+TTAATATTATAACTGAGGTTATTTTTTTAGAAAAAAGATAGCTAGCTACACGAATTATACGAGAATACATGGTCACATGCCAAGTATATTATTGTATCCT\n+TAACTACACGAAATTTATGTATTGCATGGCCACATATATGAACTATACTACGTCATGTGGCTAACATCATAGACATATAATTCCGGTATATCGACTGGTT\n+GACTCTGGCTTTGACTAACATTGACCGGCGTTGACCAACAAAAAATTTCAGAAAAAAACTTTAAAATAGTTTTTAATATTAAAAAATAAGAAACTGTTTT\n+TAGGTTTTGTATAAGAAAAAAAATTCTATTTTCAGCATAGATAGATTTGTATTTTTATCCATTAAATTTTATAATAATTAGTAAAAAGTCATTATTAAAT\n+TTTAAAATATTAAAATGGAAAAATATTATTTGAACAATTAAGTAGGAAATTGCTTAAATTTATATTGTCAATTAAAAAACCTTAATTTCTATACTATTTT\n+TATTATTATTTTGTATTTCTCAACCACAAAAATTATTAGAAGAAAACGTAATACGTATGAATTCTATTTTTATAAAAAAATTTGCTGAAATAAAAATGTT\n+AGATCAAACAACAAAATTTGTGCCTTTCTGGTTAATGTGGAGAATATGGAAGAGTAGGAATGATCTTGTATTCAACCGGAAAAGGACTGATTTCTATACT\n+ACAGTAGAATCCGCTCTCACTGACACGAAAGAATGGCTGGGTAATATACCAACGAAAGAAGATGATCAAGGAAATGCATTGTCGCCTACGAAGAGACACA\n+CTAAGTGGAGCCCCCCCCCCCCCCCCCCCCAAAAGTGATTGGCTAAAGTGCAATTATGATGCTTCTCACCATACGGGGAATACAATGTCTGGACTAGGGT\n+GGCTTATCCGCAACTCTCATGGCACGGTTTTGGAATGCGGTATGGGGTAGTTTCAAGGTCGAATGACTCCAGAAGAAGTTGAATGCTCGACACTTATCTG\n+GGCTATTCAAGCCGCTAGGGCCTATGGGTATACAAAGGTGATCTTTGAAGGTGATAACATAAATATTAATCGACTAATTAACCAGAAGTCTCCAAATCCC\n+CGACTACAACACTATCTTGATATCATATACAGTTGGATCCCAACTTTTACATCAGTAAAGTTCACCTTCAAGCATCGGGAACAAAATGCACGTGCGGATC\n+TTTTAGCTAAGAAAGCTATTTCAGCGGATACTCATTGGTCTCTGTTTCACTCATGTCCATATTTTCTTTATCATCTTGTAAACAACGATATCTCTTAAAG\n+TTCTAATAAAGTTTTTAGAAGGAAAAAAAAATGTTAGATTTTTTTTCTTTTTATAAAATAAAAGGAAAAATTGCAAGTTTTTTGTTTTATTATATTTTTA\n+ATTTAGTTTTGAAATTGAGAAAAATATATTTATATTGTATATAAAATATTTTTTTATTATACAGCAGGAAAAAATAATTCTTATTTTTTAATAATAAAAA\n+TAATTTTTAAGATTTTTTTGAATTTTTTGTTGGTCAAAGCCGGAATCAACTACTCAGTTTACCGAAATTGTATGTCTATGGTGTTAACCACATAACATCG\n+TATAGTTCATATATGTGGTCATGCAATACATCTACTTTGTGTAGCTGAAGATACAATAATATAGTTAGGCAAAGTGCATTTCACCATTACTGTTCCGGTC\n+ATAGGAAGTTTCCCTGATAGAAAAAAAAAATAACACAATGTTGCTCTTTCATAAGGAGTTGTAGACTTGACAATGTCAAATCCTTTTTTCTTTGATAACA\n+TTCATCTTCGAATTCTAAACATAATTATATCTAACGAGTAGACAAAAACTACATAACCATTGTTTCCCCTGATAAGTTGTAGCATCATATATAGCA'..b'ATCATTGTAAGTGATCAATAT\n+CTTGACAATGCTCAGATTTTCATGGCACCTGCCACCAGTGTTAATAGCTCCGTTGGCGATATTATCTACCGATATATCAACTCCACAAGGTCCTCTTTGA\n+TATTCTTGGGTATGATACTATACTACAAGTGTGTTCACAGCTAAGTAACTCTTTGTTTATGCTTTTCTCAGATCAGCGTCGGCTGTGATTCAGAAAACTC\n+GGCAAGTGACAATCCCTGCTCCATTTGTTGCTTCTTTTTCATCAAGAGGTCCCAATCCGGGATCAATACGTCTTCTCAAGGTATATATGACTTGATCAAT\n+GTCATCTGTTTATTGATAGATGATGATCTTATGTCTCTGCCATTTTTGCGGATTGTAGCCTGATATCGCTGCACCCGGGATTGATATATTGGCGGCCTTC\n+ACTCTAAAGAGATCACTGACTGGGTTAGATGGTGACACCCAGTTCTCAAAATTCACCATCCTGTCTGGCACCTCAATGGCCTGCCCTCATGTTGCTGGTG\n+TAGCTGCGTACGTCAAGTCTTTTCATCCGGATTGGACCCCTGCTGCCATCAAATCCGCCATCATTACCTCAGGTAACTCACGTCAAGTTCTCGTGAAACT\n+AAAAGCAGAGAAAGCAGTAATTATTTATCTGTTTGTTACGCAGCAAAACCGATAAGCCGGAGAGTGAACAAGGACGCAGAGTTTGCTTATGGAGGAGGCC\n+AAATAAACCCACGACGAGCCGCAAGCCCTGGCTTAGTCTACGACATGGACGACATCTCCTATGTTCAGTTCTTGTGCGGCGAAGGCTACAACGCAACCAC\n+TCTAGCTCCATTGGTGGGTACACGCTCCGTGAGCTGTTCCTCCATTGTCCCTGGACTCGGCCACGATTCCCTCAACTACCCAACAATCCAACTCACGTTG\n+AGATCCGCCAAAACGTCCACATTGGCTGTGTTCAGGCGGAGAGTCACCAACGTGGGACCACCGTCGTCGGTCTACACCGCCACCGTCCGAGCACCGAAAG\n+GAGTAGAAATCACGGTGGAGCCACAGAGTTTGTCATTTTCAAAGGCTTCACAAAAGAGAAGCTTCAAAGTGGTGGTGAAGGCCAAACAAATGACTCCTGG\n+GAAGATTGTGTCCGGCTTGCTCGTGTGGAAGAGCCCACGTCACTCTGTTCGTAGCCCCATTGTTATTTATAGTCCTACTTCGGATTGAAATTAATCACAT\n+CTCCAAAACAACATTTTACTTCAATGTAATCCTCTCACTTGTTCGTAAACTAACTCATTCCACTGCTTAATTTGAAAAAACCACTGTATTAAACTTATAG\n+GCCAATAAGCCCATATTAGAATATTTGGGCCTTTGGGCCCATTACACGAAACACTACTTACAGAATAACCTCTACCTCTCTCTCTATCGGAAAAGCCCTA\n+AAGCAAGCTTCTCTCCTTCGTCGTCAATGGAAGCTTCTCTACCGGAAGAGGTGCTTCAGCCGCTTCTACATGCTTCAGATTTATCATACTCTCTAGAAGA\n+TTGCTTGAAATTTCTTCTAGAGTCTTCCAAGACCGATTCAGGTCGTTCCGATCTCGCTTCCAAGTCTATACTTCCGTCGATCCTCCGTCTTCTTCAGCTT\n+CTTCCTTACCCATCTTCCCGCCATTATCTGAATCTCTCTCTGAAGGTCCTTCGAAACCTCTGCGCAGGTGAGGTTTCGAATCAGAACTCTTTCGTCGATC\n+ATGACGGCTCTGCTATCGTCTCCGACTTGCTTGATTCCGCCATTGCGGATTTCGAGACAGTTAGGTTCGGATTACAGGTTCTAGCGAACGTTGTATTGTT\n+CGGAGAGAAACGTCAGAGAGATGTGTGGCTCCGATTTTACCCGGAGAGGTTCTTATCAATCGCTAAGATTAGGAAACGTGAAACATTTGATCCTCTGTGT\n+ATGATTTTGTATACTTGCGTTGATGGAAGCTCAGAGATTGCTTCAGAGCTTTGTAGCTGTCAAGGGCTCACCATCATCGCTGAAACTCTACGGACTTCCT\n+CTTCCGGTAACACTCTTATTCCTGAAGCCAAAAATGCCATTTTGATCTTAAAGTCGTGATTTTTATCTGATTTGAGCCAATCTTGTTATAATTGTTTGTA\n+GTTGGGTCTGTGGAGGATTATTGGCTCAAGTTACTGGTTTCGAGAATCTGTGTTGAAGATGGTTACTTCCTCAAGCTCTTCTCTAAATTATACGAAGATG\n+CTGAAAATGAGATATTTTCATCAGAGCAAGCCTTTCTTGTGAGGATGGTGTCTGATATTGCTAATGAGCGGATAGGAAAAGTGTCAATCCCCAAGGATAC\n+AGCTTGTTCGATTCTCGGATTGTTTAGGCAATCAGTTGATGTTTTTGATTTTGTTTCGGGTGAAAGATCGGAGCTTCCAACGGGTTCAACTATAGTAGAT\n+GTGATGGGCTACTCTCTGGTGATAATAAGGGATGCTTGTGCTGGAGGACGTCTTGAAGAACTCAAGGAGGACAACAAGGATTCAGGTGATACTGTTGAAT\n+TGCTCTTGTCCTCTGGACTAATAGAACTTCTCCTTGATCTGCTTAGTAAACTTGATCCTCCAACAACAATAAAGAAGGCTTTAAACCAGAGTCCTAGTTC\n+TTCTTCTTCTTCATTAAAGCCGTGTCCTTACAGAGGATTCAGGAGAGATATTGTGTCGGTGATTGGGAACTGCGCGTACAGAAGAAAAGAGGTACAAGAT\n+GAGATCAGGGAGAGAGATGGGCTCTTTTTAATGCTGCAGCAGTGTGTGACCGATGATGAGAACCCGTTCTTGAGAGAATGGGGCTTGTGGTGTATAAGAA\n+ATTTACTGGAAGGGAACCCTGAAAACCAGGAAGTAGTGGCTGAGTTGGAGATTAAAGGCTCTGTGGATGTGCCTCAACTCCGTGAAATTGGTCTCAGGGT\n+TGAAATTGATCCTAAAACAGCCAGGCCAAAGCTTGTCAATGACACCTGAAGCTTCATTTGTCTCAGGGAAAAGAGGAGCTATACAATACACAACAAGAGG\n+TCCTTCTTGAGGCGGTGAAGATCATAAAGAAGCACGGTGTGTCGCTAGGTACCACCTGGGACAATTCTACATTGTGAGTGATCATTTTGTAGAGACAAGG\n+AATACTGATCCGGAAGCTATCTAGCTAGATGGATCCAAAACTCTGTGTTTTTGGGAAATTACAGAAAATCGTGATGACTTCTTAGGTTTCAAGAGAAAAA\n+TGTTTCATATTGGCCTTGCTTTTATTTGTTTCCTTCTTGGTATTTATAGGGTTCTAACAATTCCTATATACATGAAATGATCAATTCAATATGTTAAGCA\n+GAAAATGGCTCTCGTTTGATGTGGTTTGCAGTGCATGATCAATTAGTTCAGCTCAACTTTTGTGAAGCCTTTCATGTCTGTTGGTTTGTATTTAAGTTCC\n+TTGTTGTAAACCTTCTAAGCAGTTGTTGTGTTTCACTTTCTCTATAATAGAAAGGCAAGTTCTTCTCTATATTGTTCTGTTGACGATCAAACCAATTGTG\n+ATACAAAGTCTGATTCTCTTTCTCTGGTGTTCTGTTTCTAGAAGGAGATTCAGTTTCTAACAAGGTTCACTGCAGTCACAATTTACCGATATGCAGTCTT\n+TTCTCTGTTTTTAGATTGTTATGTTTGTTTGAGCAGAATCATGTTGAAGGTTTTCTCGAGATGTCAGCAAAAACTTACTTTACCACGGCTTGCAGACTTG\n+TACATGAAAGTTGATGATCAAACCAGGACTGATTGATTGATTGATTATACAAATGAAACCAAAAGTTCCGGAAAATACTCTGTGATAAGAATCTTATTGC\n+TCCCTGTTAACATATGGTTCAATATAACTCCAGAAAAAACCAGAGTCGTTGGCATTGAGCATTGTTGTGTGTATTCAGGAATTGTTTGATAGTCTGATT\n' |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/tool-data/fasta_indexes.loc.sample Wed May 08 08:30:21 2019 -0400 |
| b |
| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
| b |
| diff -r d3c28c4a2d16 -r 142310a198c2 epic2/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2/tool_data_table_conf.xml.sample Wed May 08 08:30:21 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |