| Previous changeset 15:c33686854b19 (2018-10-15) Next changeset 17:424aefbd7777 (2019-04-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6 |
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modified:
macs2_callpeak.xml |
| b |
| diff -r c33686854b19 -r 495a4173006f macs2_callpeak.xml --- a/macs2_callpeak.xml Mon Oct 15 06:49:16 2018 -0400 +++ b/macs2_callpeak.xml Tue Oct 16 10:31:14 2018 -0400 |
| b |
| b'@@ -167,7 +167,7 @@\n <when value="No" />\n </conditional>\n \n- <param name="format" type="select" label="Format of Input Files" help="For Paired-end BAM (BAMPE) the \'Build model step\' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions (--format). Default: Single-end BAM">\n+ <param argument="--format" type="select" label="Format of Input Files" help="For Paired-end BAM (BAMPE) the \'Build model step\' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions. Default: Single-end BAM">\n <option value="BAM" selected="True">Single-end BAM</option>\n <option value="BAMPE">Paired-end BAM</option>\n <option value="BED">Single-end BED</option>\n@@ -183,13 +183,13 @@\n <when value="create_model">\n <param name="mfold_lower" type="integer" value="5" label="Set lower mfold bound" help="Select the lower region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be higher than lower limit (--mfold). Default: 5" />\n <param name="mfold_upper" type="integer" value="50" label="Set upper mfold bound" help="Select the upper region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than the upper limit (--mfold). Default: 50"/>\n- <param name="band_width" type="integer" value="300"\n+ <param name="band_width" argument="--bw" type="integer" value="300"\n label="Band width for picking regions to compute fragment size"\n- help=" You can set this parameter as the medium fragment size expected from sonication or size selection (--bw). Default: 300" />\n+ help=" You can set this parameter as the medium fragment size expected from sonication or size selection. Default: 300" />\n </when>\n <when value="nomodel">\n- <param name="extsize" type="integer" value="200" label="Set extension size" help="The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3-prime; end, then pile them up. It is exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5-prime-to-3-prime direction to middle of fragment by 0.5 d, then extended to both direction with 0.5 d. This is equivalent to say each read is extended towards 5-prime-to-3-prime into a d size fragment. --extsize (this option) and --shift (the option below) can be combined when necessary. See --shift option below. Default: 200 (--extsize)."/>\n- <param name="shift" type="integer" value="0" label="Set shift size" help="(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5-prime) towards 5-prime-to-3-prime direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3-prime-to-5-prime direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * 0.5 of --extsize (option above) together with --extsize option for detecting enriched cutting loci such as certain DNAseI-Seq datasets. Note, you can\'t set values other than 0 if format is paired-end data (BAMPE). Default: 0 (--shift)."/>\n+ <param argument="--extsize" type="integer" value="200" label="Set extension size" help="The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3-prime; end, then pile them up. It is exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5-prime-to-3-prime direction to middle of fragment by 0.5 d, then extended'..b'4 5 6 7 8 9 **10**\n+ ======= ========= ======= ============= ==== === ======= ======== ======= =======\n chr1 840081 840400 treat1_peak_1 69 . 4.89872 10.50944 6.91052 158\n chr1 919419 919785 treat1_peak_2 87 . 5.85158 12.44148 8.70936 130\n chr1 937220 937483 treat1_peak_3 66 . 4.87632 10.06728 6.61759 154\n- ======= ========= ======= ============ ==== === ======= ======== ======= =======\n+ ======= ========= ======= ============= ==== === ======= ======== ======= =======\n \n Columns contain the following data:\n \n@@ -459,13 +457,13 @@\n \n Example:\n \n- ======= ========= ======= ============ =======\n- 1 2 3 4 **5**\n- ======= ========= ======= ============ =======\n+ ======= ========= ======= ============= =======\n+ 1 2 3 4 **5**\n+ ======= ========= ======= ============= =======\n chr1 840239 840240 treat1_peak_1 6.91052\n chr1 919549 919550 treat1_peak_2 8.70936\n chr1 937374 937375 treat1_peak_3 6.61759\n- ======= ========= ======= ============ =======\n+ ======= ========= ======= ============= =======\n \n Columns contain the following data:\n \n@@ -518,14 +516,13 @@\n \n Example:\n \n- ======= ========= ======= ============ ==== === ======= ======= =======\n- 1 2 3 4 5 6 7 8 9\n- ======= ========= ======= ============ ==== === ======= ======= =======\n- chr1 840081 840400 treat1_peak_1 52 . 4.08790 8.57605 5.21506\n- chr1 919419 919785 treat1_peak_2 56 . 4.37270 8.90436 5.60462\n- chr1 937220 937483 treat1_peak_3 48 . 4.02343 8.06676 4.86861\n- ======= ========= ======= ============ ==== === ======= ======= =======\n-\n+ ======= ====== ====== ============= ==== === ======= ======= =======\n+ 1 2 3 4 5 6 7 8 9\n+ ======= ====== ====== ============= ==== === ======= ======= =======\n+ chr1 840081 840400 treat1_peak_1 52 . 4.08790 8.57605 5.21506\n+ chr1 919419 919785 treat1_peak_2 56 . 4.37270 8.90436 5.60462\n+ chr1 937220 937483 treat1_peak_3 48 . 4.02343 8.06676 4.86861\n+ ======= ====== ====== ============= ==== === ======= ======= =======\n \n Columns contain the following data:\n \n@@ -546,13 +543,13 @@\n \n Example:\n \n- ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======\n- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15\n- ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======\n- chr1 840081 840400 treat1_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506\n- chr1 919419 919785 treat1_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462\n- chr1 937220 937483 treat1_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861\n- ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======\n+ ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15\n+ ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======\n+ chr1 840081 840400 treat1_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506\n+ chr1 919419 919785 treat1_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462\n+ chr1 937220 937483 treat1_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861\n+ ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======\n \n Columns contain the following data:\n \n' |