| Previous changeset 6:2119d851a53b (2017-04-11) Next changeset 8:e8a060164e11 (2017-12-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681 |
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modified:
macs2_bdgbroadcall.xml macs2_callpeak.xml |
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| diff -r 2119d851a53b -r f5d67c722d67 macs2_bdgbroadcall.xml --- a/macs2_bdgbroadcall.xml Tue Apr 11 17:46:41 2017 -0400 +++ b/macs2_bdgbroadcall.xml Wed Apr 12 01:47:28 2017 -0400 |
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| @@ -4,7 +4,7 @@ <import>macs2_macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="4.1.0">gnu_awk</requirement> + <requirement type="package" version="4.1.3">gawk</requirement> </expand> <expand macro="stdio" /> <expand macro="version_command" /> |
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| diff -r 2119d851a53b -r f5d67c722d67 macs2_callpeak.xml --- a/macs2_callpeak.xml Tue Apr 11 17:46:41 2017 -0400 +++ b/macs2_callpeak.xml Wed Apr 12 01:47:28 2017 -0400 |
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| @@ -29,7 +29,7 @@ @effective_genome_size@ - --bw '${$band_width}' + --bw '${band_width}' @mfold_command@ ## advanced options @@ -74,7 +74,7 @@ --extsize '${ nomodel_type.extsize }' #end if - 2> $temp_stderr) + 2>&1 > $temp_stderr) #if "peaks_tabular" in str($outputs).split(','): && cp MACS2_peaks.xls '${ output_tabular }' @@ -95,8 +95,8 @@ then mkdir '${ output_extra_files.files_path }' && cp MACS2* '${ output_extra_files.files_path }' && - python '$__tool_directory__/dir2html.py' - '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }' + python '$__tool_directory__/dir2html.py' + '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }'; fi; ) #end if @@ -251,7 +251,7 @@ <param name="cutoff_options_selector" value="qvalue"/> <param name="qvalue" value="0.05"/> <param name="band_width" value="300"/> - <param name="outputs" value="peaks_tabular,bdg"/> + <param name="outputs" value="peaks_tabular,bdg,html"/> <param name="effective_genome_size_options_selector" value="user_defined" /> <param name="gsize" value="3300000000" /> <param name="lower" value="5" /> @@ -259,6 +259,12 @@ <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/> <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/> <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/> + <output name="output_extra_files"> + <assert_contents> + <has_text text="Additional output created by MACS2" /> + </assert_contents> + </output> + </test> <test> <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> |