Mercurial > repos > nilesh > rseqc
annotate read_quality.xml @ 34:8fbd165f8835
Patch from Bjorn Gruning
| author | lparsons |
|---|---|
| date | Mon, 04 Nov 2013 16:19:36 -0500 |
| parents | 580ee0c4bc4e |
| children |
| rev | line source |
|---|---|
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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1 <tool id="rseqc_read_quality" name="Read Quality" version="1.1"> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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2 <description>determines Phred quality score</description> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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3 <requirements> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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4 <requirement type="package" version="3.0.1">R</requirement> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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5 <requirement type="package" version="1.7.1">numpy</requirement> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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6 <requirement type="package" version="2.3.7">rseqc</requirement> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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changeset
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7 </requirements> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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8 <command> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
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changeset
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9 read_quality.py -i $input -o output -r $reduce |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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changeset
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10 </command> |
| 31 | 11 <stdio> |
| 12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> | |
| 13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> | |
| 14 </stdio> | |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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15 <inputs> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
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changeset
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17 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" /> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
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changeset
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18 </inputs> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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changeset
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19 <outputs> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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changeset
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20 <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" /> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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21 <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" /> |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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22 <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" /> |
|
580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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23 </outputs> |
|
580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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24 <help> |
| 31 | 25 read_quality.py |
| 26 +++++++++++++++ | |
| 29 | 27 |
| 31 | 28 According to SAM specification, if Q is the character to represent "base calling quality" |
| 29 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that | |
| 30 returns an integer representing the Unicode code point of the character when the argument | |
| 31 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used | |
| 32 to measure "reliability" of base-calling, for example, phred quality score of 20 means | |
| 33 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there | |
| 34 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P, | |
| 35 here P is probability that base-calling is wrong. | |
| 29 | 36 |
| 37 Inputs | |
| 38 ++++++++++++++ | |
| 39 | |
| 40 Input BAM/SAM file | |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
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changeset
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41 Alignment file in BAM/SAM format. |
| 29 | 42 |
| 43 Ignore phred scores less than this number (default=1000) | |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
diff
changeset
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44 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'. |
| 29 | 45 |
| 46 Output | |
| 47 ++++++++++++++ | |
| 48 | |
| 49 1. output.qual.r | |
| 50 2. output.qual.boxplot.pdf | |
| 31 | 51 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png |
| 52 :height: 600 px | |
| 53 :width: 600 px | |
| 54 :scale: 80 % | |
| 29 | 55 3. output.qual.heatmap.pdf |
| 31 | 56 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png |
| 57 :height: 600 px | |
| 58 :width: 600 px | |
| 59 :scale: 80 % | |
| 60 | |
| 61 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density") | |
| 62 | |
| 63 ----- | |
| 64 | |
| 65 About RSeQC | |
| 66 +++++++++++ | |
| 67 | |
| 68 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. | |
| 69 | |
| 70 The RSeQC package is licensed under the GNU GPL v3 license. | |
| 71 | |
| 72 .. image:: http://rseqc.sourceforge.net/_static/logo.png | |
| 73 | |
| 74 .. _RSeQC: http://rseqc.sourceforge.net/ | |
| 75 | |
| 29 | 76 |
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580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
lparsons
parents:
31
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changeset
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77 </help> |
| 29 | 78 </tool> |