Mercurial > repos > iuc > macs2
changeset 7:da0a1fcf7fe0 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 21 Jan 2014 13:14:33 -0500 |
| parents | 97449a3c1f27 |
| children | 16dc0e3d659b |
| files | macs2_bdgbroadcall.xml macs2_bdgcmp.xml macs2_bdgdiff.xml macs2_bdgpeakcall.xml macs2_callpeak.xml macs2_filterdup.xml macs2_predict.xml macs2_randsample.xml macs2_refinepeak.xml |
| diffstat | 9 files changed, 75 insertions(+), 14 deletions(-) [+] |
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--- a/macs2_bdgbroadcall.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_bdgbroadcall.xml Tue Jan 21 13:14:33 2014 -0500 @@ -6,7 +6,6 @@ <import>macs2_macros.xml</import> </macros> <command> - macs2 bdgbroadcall --ifile $infile --cutoff-peak $cutoffpeak @@ -15,17 +14,15 @@ --lvl1-max-gap $LVL1MAXGAP --lvl2-max-gap $LVL2MAXGAP --ofile $ofile - </command> + <expand macro="stdio" /> <inputs> - <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" help="depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. DEFAULT: 2.0 (--cutoff-peak)"/> <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" help="Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1 (--cutoff-link)"/> <param name="minlen" type="integer" label="Minimum length of peak" value="200" help="better to set it as d value" /> <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" help="better to set it as tag size" /> <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" help="better to set it as 4 times of d value" /> - </inputs> <outputs>
--- a/macs2_bdgcmp.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_bdgcmp.xml Tue Jan 21 13:14:33 2014 -0500 @@ -17,6 +17,7 @@ --ofile $ofile </command> + <expand macro="stdio" /> <inputs> <!--experiment name and option of selecting paired or single end will always be present--> <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/>
--- a/macs2_bdgdiff.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_bdgdiff.xml Tue Jan 21 13:14:33 2014 -0500 @@ -29,6 +29,7 @@ --ofile-both-conditions $output_both #end if </command> + <expand macro="stdio" /> <inputs> <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" /> <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" />
--- a/macs2_bdgpeakcall.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_bdgpeakcall.xml Tue Jan 21 13:14:33 2014 -0500 @@ -6,7 +6,6 @@ <import>macs2_macros.xml</import> </macros> <command> - macs2 bdgpeakcall --ifile $infile --cutoff $cutoff @@ -15,8 +14,8 @@ $callsummits $notrackline --ofile $ofile - </command> + <expand macro="stdio" /> <inputs> <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
--- a/macs2_callpeak.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_callpeak.xml Tue Jan 21 13:14:33 2014 -0500 @@ -33,16 +33,12 @@ $advanced_options.nolambda #if str($advanced_options.broad_options.broad_options_selector) == '--broad': - #set $__options['broad'] = str( $advanced_options.broad_options.broad_options_selector ) - #set $__options['broad_cutoff'] = float( str( $advanced_options.broad_options.broad_cutoff ) ) - #end if - - #if str($advanced_options.broad_options.broad_options_selector) == '--broad': --broad --broad-cutoff='$advanced_options.broad_options.broad_cutoff' #end if #else: + ## set default parameter --mfold 10 30 #end if @@ -114,6 +110,7 @@ cat $temp_stderr 2>&1 </command> + <expand macro="stdio" /> <inputs> <param name="input_control_file" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-Seq Control File" /> <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="True" label="ChIP-Seq Treatment File" />
--- a/macs2_filterdup.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_filterdup.xml Tue Jan 21 13:14:33 2014 -0500 @@ -20,6 +20,7 @@ --keep-dup str( $keep_dup_options.keep_dup_options_selector ) #end if </command> + <expand macro="stdio" /> <inputs> <!--may need to add a few more formats at later time-->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_predict.xml Tue Jan 21 13:14:33 2014 -0500 @@ -0,0 +1,66 @@ +<tool id="macs2_predict" name="Predict" version="2.0.10.0"> + <description>d or fragment size from alignment results</description> + <expand macro="requirements"> + <requirement type="package" version="3.0.1">R_3_0_1</requirement> + </expand> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 predict + -i #echo ','.join($infiles)# + --tsize $tsize + @effective_genome_size@ + --bw $band_width + --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi + > $outfile; + + Rscript predicted_model.R > $outfile_image + </command> + <expand macro="stdio" /> + <inputs> + <repeat name="infiles" title="ChIP-seq alignment files" min="1" + help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command."> + + <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" /> + </repeat> + + <expand macro="conditional_effective_genome_size" /> + <expand macro="tag_size" /> + + <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size" + help="This value is only used while building the shifting model. (--bw)" /> + + <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5" + help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> + <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50" + help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> + + </inputs> + + <outputs> + <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" /> + <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" /> + </outputs> + <tests> + <!--none yet for macs2--> + </tests> + <help> +**What it does** + +bdgdiff from macs2 + + +Note that pair-end data is not supposed to work with this command. + + +------ + +**Citation** + +For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. + +Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. + </help> +</tool>
--- a/macs2_randsample.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_randsample.xml Tue Jan 21 13:14:33 2014 -0500 @@ -18,8 +18,8 @@ #else: $method_options.number #end if - </command> + <expand macro="stdio" /> <inputs> <!--may need to add a few more formats at later time-->
--- a/macs2_refinepeak.xml Tue Jan 21 11:50:01 2014 -0500 +++ b/macs2_refinepeak.xml Tue Jan 21 13:14:33 2014 -0500 @@ -6,7 +6,6 @@ <import>macs2_macros.xml</import> </macros> <command> - macs2 refinepeak -b $bed_infile -i $infile @@ -14,8 +13,8 @@ --cutoff $cutoff --window-size $winsize --ofile $ofile - </command> + <expand macro="stdio" /> <inputs> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />