Mercurial > repos > iuc > macs2
changeset 26:59845dc3331f draft
Uploaded
author | bgruening |
---|---|
date | Fri, 19 Sep 2014 13:43:11 -0400 |
parents | 6ed004769284 |
children | 16545befe8b5 |
files | 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 tool_dependencies.xml |
diffstat | 11 files changed, 30 insertions(+), 19 deletions(-) [+] |
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--- a/macs2_bdgbroadcall.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_bdgbroadcall.xml Fri Sep 19 13:43:11 2014 -0400 @@ -55,4 +55,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_bdgcmp.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_bdgcmp.xml Fri Sep 19 13:43:11 2014 -0400 @@ -77,4 +77,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_bdgdiff.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_bdgdiff.xml Fri Sep 19 13:43:11 2014 -0400 @@ -80,4 +80,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_bdgpeakcall.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_bdgpeakcall.xml Fri Sep 19 13:43:11 2014 -0400 @@ -56,4 +56,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_callpeak.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_callpeak.xml Fri Sep 19 13:43:11 2014 -0400 @@ -35,16 +35,11 @@ ## advanced options #if $advanced_options.advanced_options_selector == 'on': $advanced_options.nolambda - $advanced_options.call_summits #if $advanced_options.broad_options.broad_options_selector == 'broad': --broad --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }' - #end if - - #if $advanced_options.keepdup.keepdup_opt == 'specific': - --keep-dup '${ $advanced_options.keepdup.keep_duplicates }' - #else - --keep-dup '${ $advanced_options.keepdup.keepdup_opt }' + #else: + $advanced_options.broad_options.call_summits #end if #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user": @@ -91,15 +86,15 @@ #end if #if 'html' in str($outputs).split(','): - ## if output files exists, move them to the extra_files_path and create a html result page linking to them + ## if output files exists, move them to the files_path and create a html result page linking to them && ( count=`ls -1 MACS2* 2>/dev/null | wc -l`; if [ \$count != 0 ]; then - mkdir "${ output_extra_files.extra_files_path }"; - cp MACS2* "${ output_extra_files.extra_files_path }"; - python "\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.extra_files_path }" $temp_stderr > "${ output_extra_files }"; + mkdir "${ output_extra_files.files_path }"; + cp MACS2* "${ output_extra_files.files_path }"; + python "\$MACS2_SCRIPT_PATH/dir2html.py" "${ output_extra_files.files_path }" $temp_stderr > "${ output_extra_files }"; fi; ) #end if @@ -196,7 +191,7 @@ <data name="output_bed" format="bed" label="${tool.name} on ${on_string} (Peaks in BED format)"> <filter>'peaks_bed' in outputs</filter> </data> - <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)"> + <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_broad_peaks.bed" label="${tool.name} on ${on_string} (broad Peaks)"> <filter> (( advanced_options['advanced_options_selector'] == "on" and @@ -280,4 +275,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_filterdup.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_filterdup.xml Fri Sep 19 13:43:11 2014 -0400 @@ -8,7 +8,7 @@ <command> macs2 filterdup -i "${ infile }" - -o "${ outfile }" + -o temp_outfile --format '${ infile.extension.upper() }' @effective_genome_size@ @@ -19,6 +19,8 @@ #else --keep-dup "${ keep_dup_options.keep_dup_options_selector }" #end if + ; + mv temp_outfile "${ outfile }" </command> <expand macro="stdio" /> <inputs> @@ -50,4 +52,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_macros.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_macros.xml Fri Sep 19 13:43:11 2014 -0400 @@ -89,4 +89,9 @@ Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening. </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/gb-2008-9-9-r137</citation> + </citations> + </xml> </macros>
--- a/macs2_predictd.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_predictd.xml Fri Sep 19 13:43:11 2014 -0400 @@ -66,4 +66,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_randsample.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_randsample.xml Fri Sep 19 13:43:11 2014 -0400 @@ -50,4 +50,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/macs2_refinepeak.xml Wed May 21 15:34:41 2014 -0400 +++ b/macs2_refinepeak.xml Fri Sep 19 13:43:11 2014 -0400 @@ -41,4 +41,5 @@ @citation@ </help> + <expand macro="citations" /> </tool>
--- a/tool_dependencies.xml Wed May 21 15:34:41 2014 -0400 +++ b/tool_dependencies.xml Fri Sep 19 13:43:11 2014 -0400 @@ -1,16 +1,16 @@ <?xml version="1.0"?> <tool_dependency> <package name="numpy" version="1.7.1"> - <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="scipy" version="0.12.0"> - <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="1c0e86a44f73" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1c0e86a44f73" name="package_r_3_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="gnu_awk" version="4.1.0"> - <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <set_environment version="1.0"> <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> @@ -27,10 +27,10 @@ <action type="shell_command">git submodule update --recursive</action> <action type="set_environment_for_install"> - <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="numpy" version="1.7.1" /> </repository> - <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="scipy" version="0.12.0" /> </repository> </action>