Mercurial > repos > iuc > macs2
changeset 19:05aca18fd8dc draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 23 Apr 2014 18:25:51 -0400 |
| parents | ab352bb83cb2 |
| children | f63ccb331626 |
| 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, 90 insertions(+), 79 deletions(-) [+] |
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--- a/macs2_bdgbroadcall.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_bdgbroadcall.xml Wed Apr 23 18:25:51 2014 -0400 @@ -9,14 +9,15 @@ </macros> <command> macs2 bdgbroadcall - --ifile $infile - --cutoff-peak $cutoffpeak - --cutoff-link $cutofflink - --min-length $minlen - --lvl1-max-gap $LVL1MAXGAP - --lvl2-max-gap $LVL2MAXGAP - --ofile "macs2_bdgbroadcall.bdg"; - awk '!/^track name/' "macs2_bdgbroadcall.bdg" > $outfile + --ifile "${ infile }" + --cutoff-peak "${ cutoffpeak }" + --cutoff-link "${ cutofflink }" + --min-length "${ minlen }" + --lvl1-max-gap "${ LVL1MAXGAP }" + --lvl2-max-gap "${ LVL2MAXGAP }" + --ofile "macs2_bdgbroadcall.bdg" + && + awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }" </command> <expand macro="stdio" /> <inputs>
--- a/macs2_bdgcmp.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_bdgcmp.xml Wed Apr 23 18:25:51 2014 -0400 @@ -7,14 +7,14 @@ </macros> <command> macs2 bdgcmp - -t $infile_treatment - -c $infile_control + -t "${ infile_treatment }" + -c "${ infile_control }" - -m $bdgcmp_options.bdgcmp_options_selector + -m "${ bdgcmp_options.bdgcmp_options_selector }" #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']: - -p $bdgcmp_options.pseudocount + -p "${ bdgcmp_options.pseudocount }" #end if - --ofile $outfile + -o "${ outfile }" </command> <expand macro="stdio" />
--- a/macs2_bdgdiff.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_bdgdiff.xml Wed Apr 23 18:25:51 2014 -0400 @@ -7,15 +7,15 @@ </macros> <command> macs2 bdgdiff - --t1 $infile_pileup_cond1 - --t2 $infile_pileup_cond2 - --c1 $infile_control_cond1 - --c2 $infile_control_cond2 - --cutoff $cutoff - --min-len $minlen - --depth1 $depth1 - --depth2 $depth2 - --max-gap $maxgap + --t1 "${ infile_pileup_cond1 }" + --t2 "${ infile_pileup_cond2 }" + --c1 "${ infile_control_cond1 }" + --c2 "${ infile_control_cond2 }" + --cutoff "${ cutoff }" + --min-len "${ minlen }" + --depth1 "${ depth1 }" + --depth2 "${ depth2 }" + --max-gap "${ maxgap }" --o-prefix MACS2 </command>
--- a/macs2_bdgpeakcall.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_bdgpeakcall.xml Wed Apr 23 18:25:51 2014 -0400 @@ -9,14 +9,15 @@ </macros> <command> macs2 bdgpeakcall - --ifile $infile - --cutoff $cutoff - --min-length $minlen - --max-gap $maxgap - $callsummits - $notrackline - --ofile "macs2_bdgpeakcall.bdg"; - awk '!/^track name/' "macs2_bdgpeakcall.bdg" > $outfile + --ifile "${ infile }" + --cutoff "${ cutoff }" + --min-length "${ minlen }" + --max-gap "${ maxgap }" + ${ callsummits } + ${ notrackline } + --ofile "macs2_bdgpeakcall.bdg" + && + awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }" </command> <expand macro="stdio" /> <inputs>
--- a/macs2_callpeak.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_callpeak.xml Wed Apr 23 18:25:51 2014 -0400 @@ -12,17 +12,17 @@ <command> #import os #set $temp_stderr = 'macs2_stderr' - macs2 callpeak + (macs2 callpeak --name "MACS2" - -t #echo ' '.join( map(str, $input_treatment_file) )# + -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_treatment_file ) ) } - #if ' '.join( map(str, $input_control_file) ) != 'None': - -c #echo ' '.join( map(str, $input_control_file) )# + #if str( $input_control_file ) != 'None': + -t ${ ' '.join( map( lambda x:'"%s"' % ( x ), $input_control_file ) ) } #end if #for $ifile in $input_treatment_file: - --format='$ifile.ext.upper()' + --format='${ ifile.ext.upper() }' #end for @effective_genome_size@ @@ -35,7 +35,7 @@ $advanced_options.call_summits #if $advanced_options.broad_options.broad_options_selector == 'broad': --broad - --broad-cutoff='$advanced_options.broad_options.broad_cutoff' + --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }' #end if #end if @@ -46,44 +46,48 @@ ## cutoff selection #if str( $cutoff_options.cutoff_options_selector ) == 'qvalue': - --qvalue $cutoff_options.qvalue + --qvalue "${ cutoff_options.qvalue }" #elif str( $cutoff_options.cutoff_options_selector ) == 'pvalue': #if str($cutoff_options.pvalue).strip() != '': - --pvalue $cutoff_options.pvalue + --pvalue "${ cutoff_options.pvalue }" #end if #else: - --foldenrichment $cutoff_options.foldenrichment + --foldenrichment "${ cutoff_options.foldenrichment }" #end if ## model options #if $nomodel_type.nomodel_type_selector == 'nomodel': --nomodel ##--shiftsize '$nomodel_type.shiftsize' - --extsize '$nomodel_type.extsize' + --extsize '${ nomodel_type.extsize }' #end if - 2> $temp_stderr; - + 2> $temp_stderr) #if 'peaks_bed' in str($outputs).split(','): - awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3 > $output_bed; + && + awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\t' '$1=$1' | tail -n+3 > "${ output_bed }" #end if ## run R to create pdf from model script #if 'pdf' in str($outputs).split(','): - Rscript MACS2_model.r > MACS2_model.r.log; + && + Rscript MACS2_model.r > MACS2_model.r.log #end if #if 'html' in str($outputs).split(','): ## if output files exists, move them to the extra_files_path and create a html result page linking to them + && + ( 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.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 }"; fi; + ) #end if - + && cat $temp_stderr 2>&1 </command> <expand macro="stdio" />
--- a/macs2_filterdup.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_filterdup.xml Wed Apr 23 18:25:51 2014 -0400 @@ -7,17 +7,17 @@ </macros> <command> macs2 filterdup - -i $infile - -o $outfile + -i "${ infile }" + -o "${ outfile }" - --format '$infile.extension.upper()' + --format '${ infile.extension.upper() }' @effective_genome_size@ @tag_size@ - --pvalue $pvalue + --pvalue "${ pvalue }" #if str( $keep_dup_options.keep_dup_options_selector ) == "user": - --keep-dup $keep_dup_options.user_keepdup + --keep-dup "${ keep_dup_options.user_keepdup }" #else - --keep-dup $keep_dup_options.keep_dup_options_selector + --keep-dup "${ keep_dup_options.keep_dup_options_selector }" #end if </command> <expand macro="stdio" />
--- a/macs2_macros.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_macros.xml Wed Apr 23 18:25:51 2014 -0400 @@ -11,10 +11,10 @@ <xml name="conditional_effective_genome_size"> <conditional name="effective_genome_size_options"> <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize"> - <option value="3300000000">Human (3.300.000.000)</option> - <option value="3000000000">Mouse (3.000.000.000)</option> - <option value="190000000">Fly (190.000.000)</option> - <option value="130000000">Worm (130.000.000)</option> + <option value="2451960000">Human (2.451.960.000)</option> + <option value="2150570000">Mouse (2.150.570.000)</option> + <option value="121400000">Fly (121.400.000)</option> + <option value="93260000">Worm (93.260.000)</option> <option value="user_defined">User defined</option> </param> <when value="user_defined"> @@ -25,9 +25,9 @@ <token name="@effective_genome_size@"> #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': - --gsize $effective_genome_size_options.gsize + --gsize "${ effective_genome_size_options.gsize }" #else: - --gsize $effective_genome_size_options.effective_genome_size_options_selector + --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }" #end if </token> @@ -45,7 +45,7 @@ <token name="@tag_size@"> #if $tsize == -1.0: - --tsize $tsize + --tsize "${ tsize }" #end if </token>
--- a/macs2_predictd.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_predictd.xml Wed Apr 23 18:25:51 2014 -0400 @@ -10,18 +10,20 @@ </macros> <command> macs2 predictd - -i #echo ' '.join( map( str, $infiles) )# + -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) } @tag_size@ @effective_genome_size@ - --bw $band_width - --mfold $mfoldlo $mfoldhi + --bw "${ band_width }" + --mfold "${ mfoldlo }" "${ mfoldhi }" ## remove the timepoint and strip the output 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1' - > $outfile; + > "${ outfile }" + + && - Rscript predictd; + Rscript predictd </command> <expand macro="stdio" /> <inputs>
--- a/macs2_randsample.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_randsample.xml Wed Apr 23 18:25:51 2014 -0400 @@ -7,16 +7,16 @@ </macros> <command> macs2 randsample - -t $infile - -o $outfile + -t "${ infile }" + -o "${ outfile }" - --format '$infile.extension.upper()' + --format '${ infile.extension.upper() }' @tag_size@ #if $method_options.method_options_selector == 'percentage': - --percentage $method_options.percentage + --percentage "${ method_options.percentage }" #else: - --number $method_options.number + --number "${ method_options.number }" #end if </command> <expand macro="stdio" />
--- a/macs2_refinepeak.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/macs2_refinepeak.xml Wed Apr 23 18:25:51 2014 -0400 @@ -7,12 +7,12 @@ </macros> <command> macs2 refinepeak - -b $bed_infile - -i $infile - --format '$infile.extension.upper()' - --cutoff $cutoff - --window-size $winsize - --ofile $outfile + -b "${ bed_infile }" + -i "${ infile }" + --format '${ infile.extension.upper() }' + --cutoff "${ cutoff }" + --window-size "${ winsize }" + --ofile "${ outfile }" </command> <expand macro="stdio" /> <inputs>
--- a/tool_dependencies.xml Sat Feb 15 15:50:45 2014 -0500 +++ b/tool_dependencies.xml Wed Apr 23 18:25:51 2014 -0400 @@ -7,7 +7,7 @@ <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7302d8de5972" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="gnu_awk" version="4.1.0"> <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> @@ -35,8 +35,11 @@ </repository> </action> <action type="make_directory">$INSTALL_DIR/lib/python</action> + <!-- exporting the CFLAGS and CPPFLAGS are due to http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-python-package-installation-fa --> <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + export CFLAGS=-Qunused-arguments && + export CPPFLAGS=-Qunused-arguments && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin </action> <action type="set_environment">