Mercurial > repos > yating-l > regtools_junctions_extract
diff regtools_junctions_extract.xml @ 0:01ed8e112f2a draft
planemo upload commit 6bf6d4ec8ff2ec6bd45b5f483ff2f83b6229d57d
| author | yating-l |
|---|---|
| date | Wed, 12 Apr 2017 17:44:58 -0400 |
| parents | |
| children | 06d9062f5430 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/regtools_junctions_extract.xml Wed Apr 12 17:44:58 2017 -0400 @@ -0,0 +1,138 @@ +<tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.0"> + <description>Extract splice junctions from a RNA-Seq BAM file</description> + <requirements> + <requirement type="package" version="0.3.0">regtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + ## regtools expects an indexed BAM file + ## Use symlinks to link the BAM file and its index to the working directory + ## See: https://biostar.usegalaxy.org/p/10128/ + + ln -sf '${input1}' infile.bam && + ln -sf '${input1.metadata.bam_index}' infile.bam.bai && + + regtools junctions extract + -i $min_intron_length + -I $max_intron_length + -o $output1 + #if str($advanced_options.advanced_options_selector) == "on": + -a $advanced_options.min_anchor_length + + #if str($advanced_options.region): + -r "$advanced_options.region" + #end if + #end if + infile.bam && + + python $__tool_directory__/validator.py $output1 $fixed_output + ]]></command> + <inputs> + <param name="input1" type="data" format="bam" /> + + <param name="min_intron_length" type="integer" label="Minimum intron length" value="20" min="1"> + <help>Only considers spliced RNA-Seq reads with this minimum intron length (-i)</help> + </param> + <param name="max_intron_length" type="integer" label="Maximum intron length" value="500000" min="1"> + <help>Only considers spliced RNA-Seq reads with this maximum intron length (-I)</help> + </param> + + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Advanced options"> + <option value="off" selected="true">Hide advanced options</option> + <option value="on">Display advanced options</option> + </param> + <when value="on"> + <param name="min_anchor_length" type="integer" label="Minimum anchor length" value="8" min="1"> + <help>Only report splice junctions with this minimum anchor length on both sides of the junction (-a)</help> + </param> + <param name="region" type="text" optional="true" label="Only extract junctions in this region" value=""> + <help>Only report splice junctions within this region (format = chrom:start-end) (-r)</help> + <validator type="regex" + message="Region should be in the following format: chrom:start-end">^([^:]+):(\d+)-(\d+)$</validator> + </param> + </when> + + <when value="off" /> + </conditional> + </inputs> + <outputs> + <data name="output1" format="bed" label="${tool.name} on ${on_string}: original output"/> + <data name="fixed_output" format="bed" label="${tool.name} on ${on_string}: fixed_output for HAC workflow"/> + </outputs> + <tests> + <test> + <!-- Test with default parameters --> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000.bed" /> + <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_fixed.bed" /> + </test> + <test> + <!-- Test with custom intron length thresholds --> + <param name="min_intron_length" value="50" /> + <param name="max_intron_length" value="50000" /> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" file="Dbia3_adult_males_junctions_i50_I50000.bed" /> + <output name="fixed_output" file="Dbia3_adult_males_junctions_i50_I50000_fixed.bed" /> + </test> + <test> + <!-- Test with advanced option and custom anchor size --> + <param name="advanced_options_selector" value="on" /> + <param name="min_anchor_length" value="10" /> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" + file="Dbia3_adult_males_junctions_i20_I500000_a10.bed" /> + <output name="fixed_output" + file="Dbia3_adult_males_junctions_i20_I500000_a10_fixed.bed" /> + </test> + <test> + <!-- Test with advanced option and selected region --> + <param name="advanced_options_selector" value="on" /> + <param name="region" value="contig2:10000-30000" /> + <param name="input1" value="Dbia3_adult_males_shallow.bam" /> + <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed" /> + <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb_fixed.bed"/> + </test> + <test> + <!--Test with output having invalid strand --> + <param name="input1" value="Dbia3.bam" /> + <output name="output1" file="Dbia3_i20_I500000.bed" /> + <output name="fixed_output" file="Dbia3_i20_I500000_fixed.bed" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +The `regtools junctions extract <https://regtools.readthedocs.io/en/latest/commands/junctions-extract/>`_ +tool creates a list of exon-exon junctions from spliced RNA-Seq reads within a BAM +alignment file. The format of the output BED file is similar to the ``junctions.bed`` +file produced by TopHat2. + +The extent of each BED feature corresponds to the maximum overhang of each splice +junction. The score of each BED feature corresponds to the number of spliced RNA-Seq +reads that support each junction. + +-------- + +.. class:: warningmark + +By default, the minimum intron size is **20 bp** and the maximum intron size is +**500,000 bp** so that they conform to the default intron size settings for +`HISAT2 <https://ccb.jhu.edu/software/hisat2/manual.shtml#options>`_. The minimum +intron size for the command-line version of ``regtools junctions extract`` is 70 bp. + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubregtools, + author = {Griffith Lab}, + year = {2016}, + title = {regtools}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/griffithlab/regtools}, +}</citation> + </citations> +</tool>