| Previous changeset 7:8b4cb7f52809 (2019-05-08) Next changeset 9:ea03253198b4 (2020-02-03) |
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Commit message:
Uploaded 0.0.41 |
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added:
epic2 0.41/.shed.yml epic2 0.41/epic2_wrapper.xml epic2 0.41/macros.xml epic2 0.41/test-data/control.bam epic2 0.41/test-data/control.bed.gz epic2 0.41/test-data/epic2_results.txt epic2 0.41/test-data/epic2_results1.txt epic2 0.41/test-data/epic2_results2.txt epic2 0.41/test-data/epic2_results3.bed epic2 0.41/test-data/epic2_results3.txt epic2 0.41/test-data/test.bam epic2 0.41/test-data/test.bed.gz epic2 0.41/test-data/test_ChIP.bam epic2 0.41/test-data/test_Input.bam epic2 0.41/test-data/test_chromsizes.txt epic2 0.41/test-data/test_fasta.fasta epic2 0.41/tool-data/fasta_indexes.loc.sample epic2 0.41/tool_data_table_conf.xml.sample |
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removed:
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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/.shed.yml Mon Feb 03 11:43:12 2020 -0500 |
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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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/epic2_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/epic2_wrapper.xml Mon Feb 03 11:43:12 2020 -0500 |
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| b'@@ -0,0 +1,425 @@\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'eaks" 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+epic2 is an ultraperformant reimplementation of SICER, a Chip-Seq broad peak/diffuse domain finder. \n+epic2 is focused on speed, low memory overhead and ease-of-use.\n+ Software documentation may be found on https://github.com/biocore-ntnu/epic2.\n+\n+**Accepted input**\n+\n+epic2 is designed to be used with ChIP-Seq data from treatment samples, though control samples are encouraged to increase specificity. Single or multiple files are allowed as input, with same or different file formats (file extension must be bed, bedpe, bam or sam). To use multiple files as input (either as treatment or control samples), group them in a collection and select to pool files, otherwise Galaxy will run them in batch mode.\n+\n+epic2 works with only a treatment file specified as input. In this case, epic2 will run with default parameters, using the pre-indexed human genome hg19 and a FDR cutoff of 0.05. Several genomes are indexed and included on the installation of epic2, although custom genomes may be used. If your genome is not already indexed, two options are provided. One of them is to select a fasta file from which calculate chromosome sizes; the second option is to provide a tab-separated list with one chromosome name and length per row. On custom genomes, the effective genome fraction may be introduced (for more information see [deepTools](https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html)).\n+\n+**Broad peaks format**\n+\n+The output of epic2 contains called peaks in a table that does not follow any standard format. This table may be converted to BED format, assigning a unique name to each peak (islands). 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 500 when Pvalue == 0.0.\n+\n+Tool adapted to Galaxy by Miriam Pay\xc3\xa1.\n+ \n+ \n+ </help>\n+ <expand macro="citations" />\n+</tool> \n' |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/macros.xml Mon Feb 03 11:43:12 2020 -0500 |
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| @@ -0,0 +1,117 @@ +<macros> + + <token name="@VERSION@">0.0.41</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.41">epic2</requirement> + <requirement type="package">htslib</requirement> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btz232</citation> + <yield /> + </citations> + </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> + +</macros> |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/control.bam |
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| Binary file epic2 0.41/test-data/control.bam has changed |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/control.bed.gz |
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| Binary file epic2 0.41/test-data/control.bed.gz has changed |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/epic2_results.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/test-data/epic2_results.txt Mon Feb 03 11:43:12 2020 -0500 |
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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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/epic2_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/test-data/epic2_results1.txt Mon Feb 03 11:43:12 2020 -0500 |
| 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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/epic2_results2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/test-data/epic2_results2.txt Mon Feb 03 11:43:12 2020 -0500 |
| 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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/epic2_results3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/test-data/epic2_results3.bed Mon Feb 03 11:43:12 2020 -0500 |
| 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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/epic2_results3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/test-data/epic2_results3.txt Mon Feb 03 11:43:12 2020 -0500 |
| 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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/test.bam |
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| Binary file epic2 0.41/test-data/test.bam has changed |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/test.bed.gz |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/test_ChIP.bam |
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| Binary file epic2 0.41/test-data/test_ChIP.bam has changed |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/test_Input.bam |
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| Binary file epic2 0.41/test-data/test_Input.bam has changed |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/test_chromsizes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/test-data/test_chromsizes.txt Mon Feb 03 11:43:12 2020 -0500 |
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| @@ -0,0 +1,1 @@ +chr4 99999 |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2 0.41/test-data/test_fasta.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/test-data/test_fasta.fasta Mon Feb 03 11:43:12 2020 -0500 |
| 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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/tool-data/fasta_indexes.loc.sample Mon Feb 03 11:43:12 2020 -0500 |
| 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 8b4cb7f52809 -r 5f3952470864 epic2 0.41/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/epic2 0.41/tool_data_table_conf.xml.sample Mon Feb 03 11:43:12 2020 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/.shed.yml --- a/epic2/.shed.yml Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,6 +0,0 @@ -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 |
| b |
| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/epic2_wrapper.xml --- a/epic2/epic2_wrapper.xml Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,372 +0,0 @@\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' |
| b |
| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/macros.xml --- a/epic2/macros.xml Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,117 +0,0 @@ -<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">10.1093/bioinformatics/btz232</citation> - <yield /> - </citations> - </xml> - -</macros> |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/control.bam |
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| Binary file epic2/test-data/control.bam has changed |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/control.bed.gz |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/epic2_results.txt --- a/epic2/test-data/epic2_results.txt Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,166 +0,0 @@\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' |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/epic2_results1.txt --- a/epic2/test-data/epic2_results1.txt Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,166 +0,0 @@\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 8b4cb7f52809 -r 5f3952470864 epic2/test-data/epic2_results2.txt --- a/epic2/test-data/epic2_results2.txt Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -#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 8b4cb7f52809 -r 5f3952470864 epic2/test-data/epic2_results3.bed --- a/epic2/test-data/epic2_results3.bed Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -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 8b4cb7f52809 -r 5f3952470864 epic2/test-data/epic2_results3.txt --- a/epic2/test-data/epic2_results3.txt Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ -#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 |
| b |
| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/test.bam |
| b |
| Binary file epic2/test-data/test.bam has changed |
| b |
| diff -r 8b4cb7f52809 -r 5f3952470864 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 8b4cb7f52809 -r 5f3952470864 epic2/test-data/test_ChIP.bam |
| b |
| Binary file epic2/test-data/test_ChIP.bam has changed |
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| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/test_Input.bam |
| b |
| Binary file epic2/test-data/test_Input.bam has changed |
| b |
| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/test_chromsizes.txt --- a/epic2/test-data/test_chromsizes.txt Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -chr4 99999 |
| b |
| diff -r 8b4cb7f52809 -r 5f3952470864 epic2/test-data/test_fasta.fasta --- a/epic2/test-data/test_fasta.fasta Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1001 +0,0 @@\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 8b4cb7f52809 -r 5f3952470864 epic2/tool-data/fasta_indexes.loc.sample --- a/epic2/tool-data/fasta_indexes.loc.sample Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,29 +0,0 @@ -#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 8b4cb7f52809 -r 5f3952470864 epic2/tool_data_table_conf.xml.sample --- a/epic2/tool_data_table_conf.xml.sample Wed May 08 10:12:20 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<tables> - <table name="fasta_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/fasta_indexes.loc" /> - </table> -</tables> |