Mercurial > repos > iuc > tag_pileup_frequency
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"
author | iuc |
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date | Fri, 06 Dec 2019 15:32:39 -0500 |
parents | 6432735cdb22 |
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<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.2"> <description></description> <requirements> <requirement type="package" version="11.0.1">openjdk</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #import re #set input1_identifier = re.sub('[^\s\w\-]', '_', str($input1.element_identifier)) #set input2_identifier = re.sub('[^\s\w\-]', '_', str($input2.element_identifier)) mkdir -p output && ln -s '${input1}' '${input1_identifier}' && ln -s '${input2}' '${input2_identifier}' && ln -s '${input1.metadata.bam_index}' '${input1_identifier}.bai' && java -jar '$__tool_directory__/TagPileup.jar' -b '${input1_identifier}' -i '${input1_identifier}.bai' -c '$input2_identifier' -s $tag_shift -n $bin_size -e $tags_equal -r $reads -p $proper_pe -a $combine_strands -t "\${GALAXY_SLOTS:-4}" -w $composite_smoothing_window -m true -x '$output1' -h $output_heatmap #if str($output_heatmap) == "true": -o output #end if 1>/dev/null ]]></command> <inputs> <param name="input1" type="data" format="bam" label="BAM file" /> <param name="input2" type="data" format="bed" label="Bed file" /> <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" /> <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" /> <param name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" /> <param name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input"> <option value="0" selected="true">Read1</option> <option value="1">Read2</option> <option value="2">combined</option> </param> <param name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/> <param name="combine_strands" type="select" label="Combine strands?"> <option value="0" selected="true">No</option> <option value="1">Yes</option> </param> <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" /> <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" /> </inputs> <outputs> <collection name="heatmaps" type="list" label="Heatmap frequencies: ${tool.name} on ${on_string}"> <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="tabular" visible="false" /> <filter>output_heatmap == true</filter> </collection> <data name="output1" format="tabular"/> </outputs> <tests> <test> <param name="input1" value="input.bam" ftype="bam"/> <param name="input2" value="input.bed" ftype="bed"/> <param name="tag_shift" value="0" /> <param name="bin_size" value="1" /> <param name="tags_equal" value="false" /> <param name="reads" value="0" /> <param name="proper_pe" value="false" /> <param name="combine_strands" value="0" /> <param name="composite_smoothing_window" value="0" /> <param name="output_heatmap" value="true" /> <output name="output1" file="output1.tabular" ftype="tabular" compare="contains"/> <output_collection name="heatmaps" type="list"> <element name="input_bed_input_bam_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/> <element name="input_bed_input_bam_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/> </output_collection> </test> </tests> <help> **What it does** Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file. ----- **Options** **Global transformations** - **5' to 3' tag shift (bp)** - moves all tags from the 5' to the 3' direction given a specified distance in base pairs. - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows. - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons. **Read parameters** - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files). - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files). - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined). **Run parameters** - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies. - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot. </help> <citations> <citation type="bibtex"> @unpublished{None, author = {Lai, William}, title = {None}, year = {None}, eprint = {None}, url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation} }</citation> </citations> </tool>