| Previous changeset 8:e8a060164e11 (2017-12-27) Next changeset 10:f0b351e734b8 (2018-01-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2 |
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modified:
macs2_bdgbroadcall.xml macs2_bdgcmp.xml macs2_bdgdiff.xml macs2_bdgpeakcall.xml macs2_callpeak.xml macs2_filterdup.xml macs2_macros.xml macs2_predictd.xml macs2_randsample.xml macs2_refinepeak.xml |
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added:
test-data/bwa-mem-test1.bam test-data/callpeak_bampe_narrow.bed |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_bdgbroadcall.xml --- a/macs2_bdgbroadcall.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_bdgbroadcall.xml Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -8,8 +8,8 @@ </expand> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command><![CDATA[ + @home_dir@ macs2 bdgbroadcall --ifile '${ infile }' --cutoff-peak '${ cutoffpeak }' @@ -20,8 +20,7 @@ --ofile "macs2_bdgbroadcall.bdg" && awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }' - ]]> - </command> + ]]></command> <inputs> <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" /> <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_bdgcmp.xml --- a/macs2_bdgcmp.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_bdgcmp.xml Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -6,8 +6,8 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command><![CDATA[ + @home_dir@ macs2 bdgcmp -t '${ infile_treatment }' -c '${ infile_control }' @@ -17,8 +17,7 @@ -p '${ bdgcmp_options.pseudocount }' #end if -o '${ outfile }' - ]]> - </command> + ]]></command> <inputs> <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" /> <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" /> |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_bdgdiff.xml --- a/macs2_bdgdiff.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_bdgdiff.xml Thu Jan 25 02:11:52 2018 -0500 |
| [ |
| @@ -8,8 +8,8 @@ </expand> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command><![CDATA[ + @home_dir@ macs2 bdgdiff --t1 '${ t1 }' --t2 '${ t2 }' @@ -25,9 +25,7 @@ awk '!/^track name/' "c1.bed" > '${ output_cond1 }' && awk '!/^track name/' "c2.bed" > '${ output_cond1 }' && awk '!/^track name/' "both.bed" > '${ output_both }' - - ]]> - </command> + ]]></command> <inputs> <param name="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" /> <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 2" /> |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_bdgpeakcall.xml --- a/macs2_bdgpeakcall.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_bdgpeakcall.xml Thu Jan 25 02:11:52 2018 -0500 |
| [ |
| @@ -6,9 +6,8 @@ <expand macro="requirements"/> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ - + <command><![CDATA[ + @home_dir@ macs2 bdgpeakcall --ifile '${ infile }' --cutoff '${ cutoff }' @@ -17,9 +16,7 @@ ${ cutoff_analysis } ${ notrackline } --ofile '${ outfile }' - - ]]> - </command> + ]]></command> <inputs> <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0" |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_callpeak.xml --- a/macs2_callpeak.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_callpeak.xml Thu Jan 25 02:11:52 2018 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.1">\n+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.2">\n <description>Call peaks from alignment results</description>\n <macros>\n <import>macs2_macros.xml</import>\n@@ -8,6 +8,8 @@\n <expand macro="stdio" />\n <expand macro="version_command" />\n <command><![CDATA[\n+ @home_dir@\n+\n #set $temp_stderr = \'macs2_stderr\'\n (macs2 callpeak\n \n@@ -17,21 +19,8 @@\n \n #if str($treatment.t_multi_select) == "Yes":\n -t ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), \'$treatment.input_treatment_file\' ) ) }\n-\n- #if \'$treatment.input_treatment_file[0].ext.upper()\' == "BAM" and $bampe:\n- --format BAMPE\n- #else\n- --format=\'$treatment.input_treatment_file[0].ext.upper()\'\n- #end if\n-\n #else\n -t \'$treatment.input_treatment_file\'\n-\n- #if \'$treatment.input_treatment_file.ext.upper()\' == "BAM" and $bampe:\n- --format BAMPE\n- #else\n- --format=\'$treatment.input_treatment_file.ext.upper()\'\n- #end if\n #end if\n \n ## Control File(s)\n@@ -44,33 +33,41 @@\n #end if\n #end if\n \n- @effective_genome_size@\n+ --format $format\n \n- --bw \'${band_width}\'\n- @mfold_command@\n+ @effective_genome_size@\n \n ## advanced options\n- #if $advanced_options.advanced_options_selector == "on":\n- $advanced_options.nolambda\n- $advanced_options.to_large\n+\n+ $advanced_options.nolambda\n+ $advanced_options.to_large\n+\n+ #if $advanced_options.ratio:\n --ratio $advanced_options.ratio\n+ #end if\n+\n+ #if $advanced_options.slocal:\n --slocal $advanced_options.slocal\n+ #end if\n+\n+ #if $advanced_options.llocal:\n --llocal $advanced_options.llocal\n- #if $advanced_options.broad_options.broad_options_selector == "broad":\n- --broad\n- --broad-cutoff=\'${ advanced_options.broad_options.broad_cutoff }\'\n- #else\n- $advanced_options.broad_options.call_summits\n- #end if\n+ #end if\n \n- #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":\n- --keep-dup \'${ advanced_options.keep_dup_options.user_keepdup }\'\n- #else\n- --keep-dup \'${ advanced_options.keep_dup_options.keep_dup_options_selector }\'\n- #end if\n+ #if $advanced_options.broad_options.broad_options_selector == "broad":\n+ --broad\n+ --broad-cutoff=\'${ advanced_options.broad_options.broad_cutoff }\'\n+ #else\n+ $advanced_options.broad_options.call_summits\n+ #end if\n \n+ #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":\n+ --keep-dup \'${ advanced_options.keep_dup_options.user_keepdup }\'\n+ #else\n+ --keep-dup \'${ advanced_options.keep_dup_options.keep_dup_options_selector }\'\n #end if\n \n+\n ## With --bdg two additional output files will be generated.\n #if "bdg" in str($outputs).split(\',\'):\n --bdg\n@@ -89,6 +86,13 @@\n #if $nomodel_type.nomodel_type_selector == "nomodel":\n --nomodel\n --extsize \'${ nomodel_type.extsize }\'\n+ --shift \'${ nomodel_type.shift}\'\n+ #else\n+ --mfold \'${nomodel_type.mfold_lower}\' \'${nomodel_type.mfold_upper}\'\n+\n+ #if $nomodel_type.band_width:\n+ --bw \'${nomodel_type.band_width}\'\n+ #end if\n #end if\n \n 2>&1 > $temp_stderr)\n@@ -111,7 +115,7 @@\n if [ \\$count != 0 ];\n then\n mkdir \'${ output_extra_files.file'..b'the original size, about 90% or 70% of the genome size. The default hs -- 2.7e9 is recommended for UCSC human hg18 assembly. Here are all precompiled parameters for effective genome size from the MACS2_ website:\n+\n+ hs: 2.7e9\n+ mm: 1.87e9\n+ ce: 9e7\n+ dm: 1.2e8\n+\n -----\n \n **Outputs**\n \n-This tool produces a BED file of narrowPeaks as default output. It can also produce additional outputs, which can be selected under the **Additional Outputs** option above. \n+This tool produces a BED file of narrowPeaks as default output. It can also produce additional outputs, which can be selected under the **Additional Outputs** option above.\n \n * **a BED file of peaks** (default)\n * a tabular file of peaks\n@@ -366,13 +386,13 @@\n \n **Peaks BED File**\n \n-The default output is the narrowPeak BED file (BED6+4 format). This contains the peak locations, together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser. \n+The default output is the narrowPeak BED file (BED6+4 format). This contains the peak locations, together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser.\n \n Example:\n \n ======= ========= ======= ============ ==== === ======= ======== ======= =======\n 1 2 3 4 5 6 7 8 9 **10**\n- ======= ========= ======= ============ ==== === ======= ======== ======= ======= \n+ ======= ========= ======= ============ ==== === ======= ======== ======= =======\n chr1 840081 840400 MACS2_peak_1 69 . 4.89872 10.50944 6.91052 158\n chr1 919419 919785 MACS2_peak_2 87 . 5.85158 12.44148 8.70936 130\n chr1 937220 937483 MACS2_peak_3 66 . 4.87632 10.06728 6.61759 154\n@@ -394,7 +414,7 @@\n \n **Peaks tabular File**\n \n-A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. \n+A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions.\n \n Example:\n \n@@ -428,7 +448,7 @@\n \n Example:\n \n- ======= ========= ======= ============ ======= \n+ ======= ========= ======= ============ =======\n 1 2 3 4 **5**\n ======= ========= ======= ============ =======\n chr1 840239 840240 MACS2_peak_1 6.91052\n@@ -487,13 +507,13 @@\n \n Example:\n \n- ======= ========= ======= ============ ==== === ======= ======= ======= \n+ ======= ========= ======= ============ ==== === ======= ======= =======\n 1 2 3 4 5 6 7 8 9\n- ======= ========= ======= ============ ==== === ======= ======= ======= \n+ ======= ========= ======= ============ ==== === ======= ======= =======\n chr1 840081 840400 MACS2_peak_1 52 . 4.08790 8.57605 5.21506\n chr1 919419 919785 MACS2_peak_2 56 . 4.37270 8.90436 5.60462\n chr1 937220 937483 MACS2_peak_3 48 . 4.02343 8.06676 4.86861\n- ======= ========= ======= ============ ==== === ======= ======= ======= \n+ ======= ========= ======= ============ ==== === ======= ======= =======\n \n \n Columns contain the following data:\n@@ -531,14 +551,14 @@\n * **4th**: name of peak\n * **5th**: 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser\n * **6th**: strand, either "." (=no strand) or "+" or "-"\n-* **7th**: start of the first narrow peak in the region \n+* **7th**: start of the first narrow peak in the region\n * **8th**: end of the peak\n-* **9th**: RGB color key, default colour is 0 \n+* **9th**: RGB color key, default colour is 0\n * **10th**: number of blocks, including the starting 1bp and ending 1bp of broad regions\n * **11th**: length of each block, comma-separated values if multiple\n * **12th**: start of each block, comma-separated values if multiple\n-* **13th**: fold-change \n-* **14th**: -log10pvalue \n+* **13th**: fold-change\n+* **14th**: -log10pvalue\n * **15th**: -log10qvalue\n \n -----\n' |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_filterdup.xml --- a/macs2_filterdup.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_filterdup.xml Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -7,6 +7,7 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ + @home_dir@ macs2 filterdup -i '${ infile }' -o '${ outfile }' |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_macros.xml --- a/macs2_macros.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_macros.xml Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -9,23 +9,25 @@ </requirements> </xml> + <token name="@home_dir@"><![CDATA[ + export PYTHON_EGG_CACHE=`pwd` && + ]]></token> + <xml name="conditional_effective_genome_size"> <conditional name="effective_genome_size_options"> <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of Ns that should be discarded. - Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. (--gsize)"> - <option value="2451960000">H. sapiens (2,451,960,000)</option> - <option value="2150570000">M. musculus (2,150,570,000)</option> - <option value="121400000">D. melanogaster (121,400,000)</option> - <option value="93260000">C. elegans (93,260,000)</option> - <option value="12400000">S. cerevisiae (12,400,000)</option> + Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Sizes are from the MACS2 website (--gsize)"> + <option value="2700000000">H. sapiens (2.7e9)</option> + <option value="1870000000">M. musculus (1.87e9)</option> + <option value="120000000">D. melanogaster (1.2e8)</option> + <option value="90000000">C. elegans (9e7)</option> <option value="user_defined">User defined</option> </param> - <when value="2451960000" /> - <when value="2150570000" /> - <when value="121400000" /> - <when value="93260000" /> - <when value="12400000" /> + <when value="2700000000" /> + <when value="1870000000" /> + <when value="120000000" /> + <when value="90000000" /> <when value="user_defined"> <param name="gsize" type="integer" label="Effective genome size" value=""/> </when> |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_predictd.xml --- a/macs2_predictd.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_predictd.xml Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -6,8 +6,8 @@ <expand macro="requirements"/> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command><![CDATA[ + @home_dir@ macs2 predictd -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) } @@ -24,8 +24,7 @@ && Rscript predictd - ]]> - </command> + ]]></command> <inputs> <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" @@ -49,7 +48,7 @@ <param name="band_width" value="300"/> <param name="lower" value="5"/> <param name="upper" value="50"/> - <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/> + <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt" lines_diff="2"/> <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> </test> </tests> |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_randsample.xml --- a/macs2_randsample.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_randsample.xml Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -6,8 +6,8 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command><![CDATA[ + @home_dir@ macs2 randsample -t '${ infile }' -o '${ outfile }' @@ -22,8 +22,7 @@ #else: --number '${ method_options.number }' #end if - ]]> - </command> + ]]></command> <inputs> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> <expand macro="tag_size" /> |
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| diff -r e8a060164e11 -r acbd3fb47f90 macs2_refinepeak.xml --- a/macs2_refinepeak.xml Wed Dec 27 10:18:03 2017 -0500 +++ b/macs2_refinepeak.xml Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -6,8 +6,8 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command><![CDATA[ + @home_dir@ macs2 refinepeak -b '${ bed_infile }' -i '${ infile }' @@ -15,8 +15,7 @@ --cutoff '${ cutoff }' --window-size '${ winsize }' --ofile '${ outfile }' - ]]> - </command> + ]]></command> <inputs> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" /> |
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| diff -r e8a060164e11 -r acbd3fb47f90 test-data/bwa-mem-test1.bam |
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| Binary file test-data/bwa-mem-test1.bam has changed |
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| diff -r e8a060164e11 -r acbd3fb47f90 test-data/callpeak_bampe_narrow.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/callpeak_bampe_narrow.bed Thu Jan 25 02:11:52 2018 -0500 |
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| @@ -0,0 +1,1 @@ +gi|251831106|ref|NC_012920.1| 0 251 MACS2_peak_1 3056 . 44.99989 308.04297 305.64328 56 |