| Next changeset 1:68656d100a7f (2018-05-22) |
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Commit message:
planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d |
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added:
peakachu.xml test-data/test1_+xl.bam test-data/test1_-xl.bam test-data/test1_MA.png test-data/test1_peaks.tsv |
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| diff -r 000000000000 -r bc594df2aba3 peakachu.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peakachu.xml Thu Feb 15 15:59:41 2018 -0500 |
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| b'@@ -0,0 +1,195 @@\n+<tool id="peakachu" name="PEAKachu" version="0.1.0.0">\n+ <description>Calls Peaks in CLIP data</description>\n+ <requirements>\n+ <requirement type="package" version="3.6">python</requirement>\n+ <requirement type="package" version="0.1.0">peakachu</requirement>\n+ </requirements>\n+ <version_command>\n+ <![CDATA[\n+ peakachu --version\n+ ]]>\n+ </version_command>\n+ <command detect_errors="aggressive">\n+ <![CDATA[\n+ #for $i, $clib in enumerate($controlLibs):\n+ #if $clib:\n+ ln -s -f \'$clib\' ${i}.c.bam &&\n+ ln -s -f \'$clib.metadata.bam_index\' ${i}.c.bam.bai &&\n+ #end if\n+ #end for\n+ #for $j, $elib in enumerate($experimentLibs):\n+ ln -s -f \'$elib\' ${j}.e.bam &&\n+ ln -s -f \'$elib.metadata.bam_index\' ${j}.e.bam.bai &&\n+ #end for\n+\n+ pwd &&\n+ mkdir ./tmp_output && \n+ peakachu \n+ ${mode.mode_selector}\n+ --exp_libs \n+ #for $i, $elib in enumerate($experimentLibs):\n+ \'${i}.e.bam\'\n+ #end for\n+ #for $i, $clib in enumerate($controlLibs):\n+ #if $clib and $i == 0:\n+ --ctr_libs \n+ #end if\n+ #if $clib:\n+ \'${i}.c.bam\'\n+ #end if\n+ #end for\n+ $pairwise_replicates\n+ $paired_end\n+ --max_insert_size $max_insert_size\n+ --features \'$features\'\n+ --sub_features \'$sub_features\'\n+ --max_proc "\\${GALAXY_SLOTS:-1}"\n+ --output_folder ./tmp_output\n+ #if str($mode.mode_selector) == \'adaptive\':\n+ --min_cluster_expr_frac $mode.min_cluster_expr_frac\n+ --min_block_overlap $mode.min_block_overlap\n+ --min_max_block_expr $mode.min_max_block_expr\n+ #elif str($mode.mode_selector) == \'window\':\n+ --window_size $mode.window_size\n+ --step_size $mode.step_size\n+ --stat_test $mode.stat_test\n+ --het_p_val_threshold $mode.het_p_val_threshold\n+ --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold\n+ #end if\n+ --norm_method $mode.norm_method.norm_method_selector\n+ #if str($mode.norm_method.norm_method_selector) == \'manual\':\n+ --size_factors $size_factors\n+ #end if\n+ --mad_multiplier $mad_multiplier\n+ --fc_cutoff $fc_cutoff\n+ --padj_threshold $padj_threshold\n+\n+ &&\n+ head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&\n+ tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&\n+ mv peaks.tsv \'$peak_tables\' &&\n+ mv ./tmp_output/plots/Initial*.png \'$MA_plot\'\n+\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param name="experimentLibs" type="data" format="bam" label="Experiment Libraries" multiple="True"/>\n+ <param name="controlLibs" type="data" format="bam" label="Control Libraries" multiple="True" optional="True"/>\n+ <param argument="--pairwise_replicates" type="boolean" truevalue="--pairwise_replicates" falsevalue="" checked="False" label="Pairwise Replicates" /> \n+ <param argument="--paired_end" type="boolean" truevalue="--paired_end" falsevalue="" checked="False" label="Paired End" /> \n+ <param argument="--max_insert_size" type="integer" value="50" label="Maximum Insert Size"/>\n+ <!-- The gff feature is not implemented, because the function can easily be accomplished with featureCount or other tools\n+ <param name="gffs" type="data" format="gff" label="Annotation" optional="True" multiple="True"/-->\n+ <param argument="--features" type="text" label="Features">\n+ <sanitizer>\n+ <valid initial="default"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="--sub_features" type="text" label="Sub-Features">\n+ <sanitizer>\n+ <valid initial="default"/>\n+ </sanitizer>\n+ </param>\n+\n+ '..b'/sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="window">\n+ <param argument="--window_size" label="Window Size" type="integer" value="25"/>\n+ <param argument="--step_size" label="Step Size" type="integer" value="5"/>\n+ <param name="stat_test" type="select" label="Statistical Test">\n+ <option value="gtest" selected="True">gtest</option>\n+ <option value="deseq">DESeq2</option>\n+ </param>\n+ <conditional name="norm_method">\n+ <param name="norm_method_selector" type="select" label="Normalisation Method.">\n+ <option value="tmm" selected="True">TMM</option>\n+ <option value="deseq">DESeq2</option>\n+ <option value="count">Count</option>\n+ <option value="manual">Manual</option>\n+ <option value="none">None</option>\n+ </param>\n+ <when value="deseq"/>\n+ <when value="tmm"/>\n+ <when value="count"/>\n+ <when value="none"/>\n+ <when value="manual">\n+ <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE">\n+ <sanitizer>\n+ <valid initial="default"/>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ <param argument="--het_p_val_threshold" label="Heterogeneous p-value Threshold" type="float" value="0.01"/>\n+ <param argument="--rep_pair_p_val_threshold" label="Paired p-value Threshold" type="float" value="0.05"/>\n+ </when>\n+ </conditional>\n+ <param argument="--mad_multiplier" label="Mad Multiplier" type="float" value="2.0"/>\n+ <param argument="--fc_cutoff" label="Fold Change Threshold" type="float" value="2.0"/>\n+ <param argument="--padj_threshold" type="float" label="Adjusted p-value Threshold" value="0.05"/> \n+ </inputs>\n+ <outputs>\n+ <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/>\n+ <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="experimentLibs" value="test1_+xl.bam"/>\n+ <param name="controlLibs" value="test1_-xl.bam"/>\n+ <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>\n+ <output name="MA_plot" ftype="png" file="test1_MA.png"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+**PEAKachu**\n+\n+PEAKachu is a tool for the accurate mapping of RBP binding sites based on CLIP-seq and RIP-seq data.\n+PEAKachu uses signal and control libraries (ideally more than three each) to detect binding sites.\n+It implements two peak calling approaches\n+\n+**adaptive**\n+\n+The adaptive approach applies a three-step procedure to detect regions that are significantly enriched over controls.\n+\n+- blockbuster is applied to the pooled libraries to combine similar sets of reads into blocks\n+- blocks are decomposed into peaks by iteratively applying a block merging heuristic\n+- peaks with significant enrichment of signal over control libraries are determined using DESeq2\n+\n+**windowed**\n+\n+The windowed approach subdivides the genome into overlapping regions.\n+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.\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r bc594df2aba3 test-data/test1_peaks.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_peaks.tsv Thu Feb 15 15:59:41 2018 -0500 |
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| @@ -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 |
