# HG changeset patch # User iuc # Date 1486366237 18000 # Node ID 56e10499997855fd981cc5a8425df01c4eb9a03e # Parent 6d4babad010f5873828104c66ce3c5f1a33eba31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e diff -r 6d4babad010f -r 56e104999978 dir2html.py --- a/dir2html.py Wed Jan 27 15:23:25 2016 -0500 +++ b/dir2html.py Mon Feb 06 02:30:37 2017 -0500 @@ -1,38 +1,43 @@ -#!/usr/bin/env python -import os -import sys -from xml.sax.saxutils import escape - -def make_table( directory ): - ret = ['\n'] - for file in os.listdir( directory ): - ret.append('\n' % ( file, escape(file).replace( 'MACS2_', '' ) )) - ret.append('
%s
') - return ''.join(ret) - -def make_html( directory, stderr ): - return '\n'.join(['' - '', - ' Additional output created by MACS2', - ' ', - '', - '', - '

Additional Files:

', - make_table( directory ), - '

Messages from MACS2:

', - stderr.read().replace('\n', '
'), - '', - '']) - -if __name__ == '__main__': - if len(sys.argv) == 3: - directory_path = sys.argv[1] - stderr = open( sys.argv[2] ) - print make_html( directory_path, stderr ) - else: - sys.exit( 'Two parameter expected: directory path and stderr path' ) - +#!/usr/bin/env python + +from __future__ import print_function + +import os +import sys +from xml.sax.saxutils import escape + + +def make_table(directory): + ret = ['\n'] + for filename in os.listdir(directory): + ret.append('\n' % (filename, escape(filename).replace('MACS2_', ''))) + ret.append('
%s
') + return ''.join(ret) + + +def make_html(directory, stderr): + return '\n'.join(['' + '', + ' Additional output created by MACS2', + ' ', + '', + '', + '

Additional Files:

', + make_table(directory), + '

Messages from MACS2:

', + stderr.read().replace('\n', '
'), + '', + '']) + + +if __name__ == '__main__': + if len(sys.argv) == 3: + directory_path = sys.argv[1] + stderr = open(sys.argv[2]) + print(make_html(directory_path, stderr)) + else: + sys.exit('Two parameter expected: directory path and stderr path') diff -r 6d4babad010f -r 56e104999978 macs2_bdgdiff.xml --- a/macs2_bdgdiff.xml Wed Jan 27 15:23:25 2016 -0500 +++ b/macs2_bdgdiff.xml Mon Feb 06 02:30:37 2017 -0500 @@ -33,11 +33,10 @@ - + - diff -r 6d4babad010f -r 56e104999978 macs2_callpeak.xml --- a/macs2_callpeak.xml Wed Jan 27 15:23:25 2016 -0500 +++ b/macs2_callpeak.xml Mon Feb 06 02:30:37 2017 -0500 @@ -66,8 +66,6 @@ #if str($cutoff_options.pvalue).strip() != '': --pvalue "${ cutoff_options.pvalue }" #end if - #else: - --foldenrichment "${ cutoff_options.foldenrichment }" #end if ## model options @@ -121,7 +119,6 @@ - - - - @@ -150,14 +143,13 @@ - + - diff -r 6d4babad010f -r 56e104999978 test-data/output_extra_files.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_extra_files.html Mon Feb 06 02:30:37 2017 -0500 @@ -0,0 +1,22 @@ + + Additional output created by MACS2 + + + +

Additional Files:

+ + + + + + + +
model.pdf
summits.bed
model.r
peaks.narrowPeak
model.r.log
peaks.xls
+

Messages from MACS2:

+INFO @ Tue, 24 Jan 2017 12:19:10:
# Command line: callpeak --name MACS2 -t /tmp/tmp1QIUtc/files/000/dataset_1.dat -c /tmp/tmp1QIUtc/files/000/dataset_2.dat --format=BED --gsize 3300000000 --bw=300 --qvalue 0.05
# ARGUMENTS LIST:
# name = MACS2
# format = BED
# ChIP-seq file = ['/tmp/tmp1QIUtc/files/000/dataset_1.dat']
# control file = ['/tmp/tmp1QIUtc/files/000/dataset_2.dat']
# effective genome size = 3.30e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# Paired-End mode is off

INFO @ Tue, 24 Jan 2017 12:19:10: #1 read tag files...
INFO @ Tue, 24 Jan 2017 12:19:10: #1 read treatment tags...
INFO @ Tue, 24 Jan 2017 12:19:10: #1.2 read input tags...
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tag size is determined as 100 bps
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tag size = 100
INFO @ Tue, 24 Jan 2017 12:19:10: #1 total tags in treatment: 199977
INFO @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags...
INFO @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tags after filtering in treatment: 199583
INFO @ Tue, 24 Jan 2017 12:19:10: #1 Redundant rate of treatment: 0.00
INFO @ Tue, 24 Jan 2017 12:19:10: #1 total tags in control: 199978
INFO @ Tue, 24 Jan 2017 12:19:10: #1 user defined the maximum tags...
INFO @ Tue, 24 Jan 2017 12:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Tue, 24 Jan 2017 12:19:10: #1 tags after filtering in control: 199867
INFO @ Tue, 24 Jan 2017 12:19:10: #1 Redundant rate of control: 0.00
INFO @ Tue, 24 Jan 2017 12:19:10: #1 finished!
INFO @ Tue, 24 Jan 2017 12:19:10: #2 Build Peak Model...
INFO @ Tue, 24 Jan 2017 12:19:10: #2 looking for paired plus/minus strand peaks...
INFO @ Tue, 24 Jan 2017 12:19:11: #2 number of paired peaks: 4488
INFO @ Tue, 24 Jan 2017 12:19:11: start model_add_line...
INFO @ Tue, 24 Jan 2017 12:19:11: start X-correlation...
INFO @ Tue, 24 Jan 2017 12:19:11: end of X-cor
INFO @ Tue, 24 Jan 2017 12:19:11: #2 finished!
INFO @ Tue, 24 Jan 2017 12:19:11: #2 predicted fragment length is 254 bps
INFO @ Tue, 24 Jan 2017 12:19:11: #2 alternative fragment length(s) may be 254 bps
INFO @ Tue, 24 Jan 2017 12:19:11: #2.2 Generate R script for model : MACS2_model.r
INFO @ Tue, 24 Jan 2017 12:19:11: #3 Call peaks...
INFO @ Tue, 24 Jan 2017 12:19:11: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 24 Jan 2017 12:19:12: #3 Call peaks for each chromosome...
INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write output xls file... MACS2_peaks.xls
INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak
INFO @ Tue, 24 Jan 2017 12:19:13: #4 Write summits bed file... MACS2_summits.bed
INFO @ Tue, 24 Jan 2017 12:19:13: Done!
+ + diff -r 6d4babad010f -r 56e104999978 tool_dependencies.xml --- a/tool_dependencies.xml Wed Jan 27 15:23:25 2016 -0500 +++ b/tool_dependencies.xml Mon Feb 06 02:30:37 2017 -0500 @@ -7,13 +7,13 @@ - + - + $REPOSITORY_INSTALL_DIR