Mercurial > repos > bgruening > peakachu
changeset 0:28c319539b42 draft default tip
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
| author | bgruening |
|---|---|
| date | Thu, 15 Feb 2018 11:09:43 -0500 |
| parents | |
| children | |
| files | peakachu.xml test-data/test1_+xl.bam test-data/test1_-xl.bam test-data/test1_MA.png test-data/test1_peaks.tsv |
| diffstat | 5 files changed, 198 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peakachu.xml Thu Feb 15 11:09:43 2018 -0500 @@ -0,0 +1,195 @@ +<tool id="peakachu" name="PEAKachu" version="0.1.0.0"> + <description>Calls Peaks in CLIP data</description> + <requirements> + <requirement type="package" version="3.6">python</requirement> + <requirement type="package" version="0.1.0">peakachu</requirement> + </requirements> + <version_command> + <![CDATA[ + peakachu --version + ]]> + </version_command> + <command detect_errors="aggressive"> + <![CDATA[ + #for $i, $clib in enumerate($controlLibs): + #if $clib: + ln -s -f '$clib' ${i}.c.bam && + ln -s -f '$clib.metadata.bam_index' ${i}.c.bam.bai && + #end if + #end for + #for $j, $elib in enumerate($experimentLibs): + ln -s -f '$elib' ${j}.e.bam && + ln -s -f '$elib.metadata.bam_index' ${j}.e.bam.bai && + #end for + + pwd && + mkdir ./tmp_output && + peakachu + ${mode.mode_selector} + --exp_libs + #for $i, $elib in enumerate($experimentLibs): + '${i}.e.bam' + #end for + #for $i, $clib in enumerate($controlLibs): + #if $clib and $i == 0: + --ctr_libs + #end if + #if $clib: + '${i}.c.bam' + #end if + #end for + $pairwise_replicates + $paired_end + --max_insert_size $max_insert_size + --features '$features' + --sub_features '$sub_features' + --max_proc "\${GALAXY_SLOTS:-1}" + --output_folder ./tmp_output + #if str($mode.mode_selector) == 'adaptive': + --min_cluster_expr_frac $mode.min_cluster_expr_frac + --min_block_overlap $mode.min_block_overlap + --min_max_block_expr $mode.min_max_block_expr + #elif str($mode.mode_selector) == 'window': + --window_size $mode.window_size + --step_size $mode.step_size + --stat_test $mode.stat_test + --het_p_val_threshold $mode.het_p_val_threshold + --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold + #end if + --norm_method $mode.norm_method.norm_method_selector + #if str($mode.norm_method.norm_method_selector) == 'manual': + --size_factors $size_factors + #end if + --mad_multiplier $mad_multiplier + --fc_cutoff $fc_cutoff + --padj_threshold $padj_threshold + + && + head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv && + tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv && + mv peaks.tsv '$peak_tables' && + mv ./tmp_output/plots/Initial*.png '$MA_plot' + + ]]> + </command> + <inputs> + <param name="experimentLibs" type="data" format="bam" label="Experiment Libraries" multiple="True"/> + <param name="controlLibs" type="data" format="bam" label="Control Libraries" multiple="True" optional="True"/> + <param argument="--pairwise_replicates" type="boolean" truevalue="--pairwise_replicates" falsevalue="" checked="False" label="Pairwise Replicates" /> + <param argument="--paired_end" type="boolean" truevalue="--paired_end" falsevalue="" checked="False" label="Paired End" /> + <param argument="--max_insert_size" type="integer" value="50" label="Maximum Insert Size"/> + <!-- The gff feature is not implemented, because the function can easily be accomplished with featureCount or other tools + <param name="gffs" type="data" format="gff" label="Annotation" optional="True" multiple="True"/--> + <param argument="--features" type="text" label="Features"> + <sanitizer> + <valid initial="default"/> + </sanitizer> + </param> + <param argument="--sub_features" type="text" label="Sub-Features"> + <sanitizer> + <valid initial="default"/> + </sanitizer> + </param> + + <conditional name="mode"> + <param name="mode_selector" type="select" label="Select Mode" help="These modes work differently."> + <option value="adaptive" selected="True">Adaptive</option> + <option value="window">Window</option> + <!-- The following options are not implemented because they are vastly different and should be implemented as their own tool, if need be. + <option value="coverage">Coverage</option> + <option value="consensus_peak">Consensus Peak</option--> + </param> + <when value="adaptive"> + <param argument="--min_cluster_expr_frac" label="Minimum cluster Expression Fraction" help="Minimum fraction of a block in a cluster for further consideration." type="float" value="0.01"/> + <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/> + <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/> + <conditional name="norm_method"> + <param name="norm_method_selector" type="select" label="Normalisation Method."> + <option value="deseq" selected="True">DESeq2</option> + <option value="manual">Manual</option> + <option value="none">None</option> + </param> + <when value="deseq"/> + <when value="none"/> + <when value="manual"> + <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE"> + <sanitizer> + <valid initial="default"/> + </sanitizer> + </param> + </when> + </conditional> + </when> + <when value="window"> + <param argument="--window_size" label="Window Size" type="integer" value="25"/> + <param argument="--step_size" label="Step Size" type="integer" value="5"/> + <param name="stat_test" type="select" label="Statistical Test"> + <option value="gtest" selected="True">gtest</option> + <option value="deseq">DESeq2</option> + </param> + <conditional name="norm_method"> + <param name="norm_method_selector" type="select" label="Normalisation Method."> + <option value="tmm" selected="True">TMM</option> + <option value="deseq">DESeq2</option> + <option value="count">Count</option> + <option value="manual">Manual</option> + <option value="none">None</option> + </param> + <when value="deseq"/> + <when value="tmm"/> + <when value="count"/> + <when value="none"/> + <when value="manual"> + <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE"> + <sanitizer> + <valid initial="default"/> + </sanitizer> + </param> + </when> + </conditional> + <param argument="--het_p_val_threshold" label="Heterogeneous p-value Threshold" type="float" value="0.01"/> + <param argument="--rep_pair_p_val_threshold" label="Paired p-value Threshold" type="float" value="0.05"/> + </when> + </conditional> + <param argument="--mad_multiplier" label="Mad Multiplier" type="float" value="2.0"/> + <param argument="--fc_cutoff" label="Fold Change Threshold" type="float" value="2.0"/> + <param argument="--padj_threshold" type="float" label="Adjusted p-value Threshold" value="0.05"/> + </inputs> + <outputs> + <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/> + <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/> + </outputs> + <tests> + <test> + <param name="experimentLibs" value="test1_+xl.bam"/> + <param name="controlLibs" value="test1_-xl.bam"/> + <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/> + <output name="MA_plot" ftype="png" file="test1_MA.png"/> + </test> + </tests> + <help> + <![CDATA[ +**PEAKachu** + +PEAKachu is a tool for the accurate mapping of RBP binding sites based on CLIP-seq and RIP-seq data. +PEAKachu uses signal and control libraries (ideally more than three each) to detect binding sites. +It implements two peak calling approaches + +**adaptive** + +The adaptive approach applies a three-step procedure to detect regions that are significantly enriched over controls. + +- blockbuster is applied to the pooled libraries to combine similar sets of reads into blocks +- blocks are decomposed into peaks by iteratively applying a block merging heuristic +- peaks with significant enrichment of signal over control libraries are determined using DESeq2 + +**windowed** + +The windowed approach subdivides the genome into overlapping regions. +After filtering of lowly expressed regions and library normalization (either using manual size factors, TMM, or DESeq2), this approach determines significantly enriched windows using eiterh DESeq2 or repeated G-tests of goodness-of-fit. + + ]]> + </help> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_peaks.tsv Thu Feb 15 11:09:43 2018 -0500 @@ -0,0 +1,3 @@ +replicon peak_id peak_start peak_end peak_strand 0.e 0.c base_means fold_change feature_type feature_start feature_end feature_strand feature_locus_tag feature_name subfeature_type feature_product overlap_length +NC_016810.1 1 514559 514582 - 72.56031973468696 18.605210188381267 45.58276496153411 3.900000000000001 intergenic NA NA NA NA NA NA NA NA +NC_016810.1 2 514559 514584 + 70.94786818502725 18.605210188381267 44.776539186704255 3.813333333333334 intergenic NA NA NA NA NA NA NA NA