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Changeset 8:e8a060164e11 (2017-12-27)

Previous changeset 7:f5d67c722d67 (2017-04-12) Next changeset 9:acbd3fb47f90 (2018-01-25)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90

modified:
macs2_callpeak.xml
macs2_macros.xml

diff -r f5d67c722d67 -r e8a060164e11 macs2_callpeak.xml
--- a/macs2_callpeak.xml Wed Apr 12 01:47:28 2017 -0400
+++ b/macs2_callpeak.xml Wed Dec 27 10:18:03 2017 -0500

[

b'@@ -1,4 +1,4 @@\n-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.0">\n+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.1">\n <description>Call peaks from alignment results</description>\n <macros>\n <import>macs2_macros.xml</import>\n@@ -7,25 +7,42 @@\n </expand>\n <expand macro="stdio" />\n <expand macro="version_command" />\n- <command>\n- <![CDATA[\n+ <command><![CDATA[\n #set $temp_stderr = \'macs2_stderr\'\n (macs2 callpeak\n \n --name \'MACS2\'\n- -t ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), $input_treatment_file ) ) }\n+\n+ ## Treatment File(s)\n+\n+ #if str($treatment.t_multi_select) == "Yes":\n+ -t ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), \'$treatment.input_treatment_file\' ) ) }\n \n- #if str( $input_control_file ) != \'None\':\n- -c ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), $input_control_file ) ) }\n+ #if \'$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- #for $ifile in $input_treatment_file:\n- #if $ifile.ext.upper() == "BAM" and $bampe:\n- --format BAMPE\n- #else\n- --format=\'$ifile.ext.upper()\'\n+ ## Control File(s)\n+\n+ #if str($control.c_select) == "Yes":\n+ #if str($control.c_multiple.c_multi_select) == "Yes":\n+ -c ${ \' \'.join( map( lambda x:\'"%s"\' % ( x ), \'$control.c_multiple.input_control_file\' ) ) }\n+ #else\n+ -c \'$control.c_multiple.input_control_file\'\n+ #end if\n #end if\n- #end for\n \n @effective_genome_size@\n \n@@ -42,7 +59,7 @@\n #if $advanced_options.broad_options.broad_options_selector == "broad":\n --broad\n --broad-cutoff=\'${ advanced_options.broad_options.broad_cutoff }\'\n- #else:\n+ #else\n $advanced_options.broad_options.call_summits\n #end if\n \n@@ -104,13 +121,42 @@\n exit_code_for_galaxy=\\$? &&\n cat $temp_stderr 2>&1 &&\n (exit \\$exit_code_for_galaxy)\n- ]]>\n- </command>\n+ ]]></command>\n <inputs>\n- <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="true"\n- label="ChIP-Seq Treatment File" />\n- <param name="input_control_file" type="data" format="bam,sam,bed" multiple="true" optional="True"\n- label="ChIP-Seq Control File" />\n+ <conditional name="treatment">\n+ <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >\n+ <option value="No" selected="True">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <when value="No" >\n+ <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" />\n+ </when>\n+ <when value="Yes">\n+ <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" />\n+ </when>\n+ </conditional>\n+\n+ <conditional name="control">\n+ <param name="c_select" type="select" label="Do you have a Control File?" >\n+ <option value="Yes" selected="True'..b'an be loaded directly to UCSC genome browser.\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 MACS2_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506\n+ chr1 919419 919785 MACS2_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462\n+ chr1 937220 937483 MACS2_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+* **1st**: chromosome name\n+* **2nd**: start position of peak\n+* **3rd**: end position of peak\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+* **8th**: end of the peak\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+* **15th**: -log10qvalue\n+\n+-----\n+\n+**More Information**\n+\n MACS2 performs the following analysis steps:\n \n- * Artificially extend reads to expected fragment length, and generate coverage map along genome.\n- * Assume background reads are Poisson distributed. Mean of the Poisson is locally variable and is estimated from control experiment (if available) in 5Kbp or 10Kbp around examined location.\n- * For a given location, do we see more reads than we would have expected from the Poisson (p < 0.00005)? If Yes, MACS2 calls a peak. \n+ * Artificially extends reads to expected fragment length, and generates coverage map along genome.\n+ * Assumes background reads are Poisson distributed. Mean of the Poisson is locally variable and is estimated from control experiment (if available) in 5Kbp or 10Kbp around examined location.\n+ * For a given location, asks do we see more reads than we would have expected from the Poisson (p < 0.00005)? If Yes, MACS2 calls a peak.\n+\n \n+**Tips of fine-tuning peak calling**\n+\n+Check out these other MACS2 tools:\n+\n+ * **MACS2 bdgcmp** can be used on the callpeak bedGraph files or bedGraph files from other resources to calculate score track.\n+ * **MACS2 bdgpeakcall** can be used on the file generated from bdgcmp or bedGraph file from other resources to call peaks with given cutoff, maximum-gap between nearby mergable peaks and minimum length of peak. bdgbroadcall works similarly to bdgpeakcall, however it will output a broad peaks file in BED12 format.\n+ * Differential calling tool **MACS2 bdgdiff**, can be used on 4 bedGraph files which are scores between treatment 1 and control 1, treatment 2 and control 2, treatment 1 and treatment 2, treatment 2 and treatment 1. It will output the consistent and unique sites according to parameter settings for minimum length, maximum gap and cutoff.\n \n .. class:: warningmark\n \n-If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options.\n+If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website.\n \n+.. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html\n \n @citation@\n-]]>\n- </help>\n+]]></help>\n <expand macro="citations" />\n </tool>\n'

diff -r f5d67c722d67 -r e8a060164e11 macs2_macros.xml
--- a/macs2_macros.xml Wed Apr 12 01:47:28 2017 -0400
+++ b/macs2_macros.xml Wed Dec 27 10:18:03 2017 -0500

@@ -4,6 +4,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION_STRING@">macs2</requirement>
+            <requirement type="package" version="3.4">r-base</requirement>
             <yield />
         </requirements>
     </xml>