Mercurial > repos > nilesh > rseqc
diff read_quality.xml @ 3:71ed55a3515a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
| author | iuc |
|---|---|
| date | Tue, 14 Mar 2017 10:22:57 -0400 |
| parents | f92b87abef3d |
| children | caaa120457bc |
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--- a/read_quality.xml Thu Jul 18 11:01:08 2013 -0500 +++ b/read_quality.xml Tue Mar 14 10:22:57 2017 -0400 @@ -1,58 +1,92 @@ -<tool id="read_quality" name="Read Quality"> - <description>determines Phred quality score</description> - <requirements> - <requirement type="package" version="2.15.1">R</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements> - <command interpreter="python"> read_quality.py -i $input -o output -r $reduce - </command> - <inputs> - <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> - <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" /> - </inputs> - <outputs> - <data format="r" name="outputr" from_work_dir="output.qual.r" /> - <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" /> - <data format="pdf" name="outputbxpdf" from_work_dir="output.qual.boxplot.pdf" /> - </outputs> - <tests> - <test> - <param name="input" value="Pairend_nonStrandSpecific_36mer_Human_hg19.bam" /> - <output name="outputr" file="readqualout.qual.r" /> - <output name="outputpdf" file="readqualout.qual.heatmap.pdf" /> - <output name="outputbxpdf" file="readqualout.qual.boxplot.pdf" /> - </test> - </tests> - <help> -.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062 +<tool id="rseqc_read_quality" name="Read Quality" version="@WRAPPER_VERSION@"> + <description>determines Phred quality score</description> + + <macros> + <import>rseqc_macros.xml</import> + </macros> + + <expand macro="requirements" /> + + <expand macro="stdio" /> + + <version_command><![CDATA[read_quality.py --version]]></version_command> + + <command><![CDATA[ + read_quality.py + --input-file '${input}' + --out-prefix output + -r ${reduce} + --mapq ${mapq} + ]]> + </command> + + <inputs> + <expand macro="bam_sam_param" /> + <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/> + <expand macro="mapq_param" /> + <expand macro="rscript_output_param" /> + </inputs> ------ + <outputs> + <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" /> + <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" /> + <expand macro="rscript_output_data" filename="output.qual.r" /> + </outputs> -About RSeQC -+++++++++++ + <tests> + <test> + <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/> + <param name="rscript_output" value="true" /> + <output name="outputr" file="output.qual.r"/> + <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" /> + <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" /> + </test> + </tests> -The RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation. + <help><![CDATA[ +read_quality.py ++++++++++++++++ -The RSeQC package is licensed under the GNU GPL v3 license. +According to SAM specification, if Q is the character to represent "base calling quality" +in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that +returns an integer representing the Unicode code point of the character when the argument +is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used +to measure "reliability" of base-calling, for example, phred quality score of 20 means +there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there +is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P, +here P is probability that base-calling is wrong. Inputs ++++++++++++++ Input BAM/SAM file - Alignment file in BAM/SAM format. + Alignment file in BAM/SAM format. Ignore phred scores less than this number (default=1000) - To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'. + To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'. Output ++++++++++++++ 1. output.qual.r 2. output.qual.boxplot.pdf -.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/36mer.qual.plot.png + .. image:: $PATH_TO_IMAGES/36mer.qual.plot.png + :height: 600 px + :width: 600 px + :scale: 80 % 3. output.qual.heatmap.pdf -.. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/36mer.qual.heatmap.png -use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density") + .. image:: $PATH_TO_IMAGES/36mer.qual.heatmap.png + :height: 600 px + :width: 600 px + :scale: 80 % + +Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density") - </help> +@ABOUT@ + +]]> + </help> + + <expand macro="citations" /> + </tool>