annotate clipping_profile.xml @ 32:580ee0c4bc4e

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
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children
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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
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1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="1.1">
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2 <description>
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3 estimates clipping profile of RNA-seq reads from BAM or SAM file
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="3.0.1">R</requirement>
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7 <requirement type="package" version="1.7.1">numpy</requirement>
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8 <requirement type="package" version="2.3.7">rseqc</requirement>
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9 </requirements>
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10 <command>
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11 clipping_profile.py -i $input -o output
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12 </command>
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13 <stdio>
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14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
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15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
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16 </stdio>
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17 <inputs>
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18 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
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19 </inputs>
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20 <outputs>
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21 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
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22 <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
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23 </outputs>
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24 <help>
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25 clipping_profile.py
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26 +++++++++++++++++++
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28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
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29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
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30 (This means your reads aligner should support clipped mapping).
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32 Inputs
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33 ++++++++++++++
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34
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35 Input BAM/SAM file
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36 Alignment file in BAM/SAM format.
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39 Sample Output
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40 ++++++++++++++
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41
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42 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
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43 :height: 600 px
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44 :width: 600 px
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45 :scale: 80 %
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46
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47 -----
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48
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49 About RSeQC
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50 +++++++++++
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51
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52 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.
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53
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54 The RSeQC package is licensed under the GNU GPL v3 license.
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55
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56 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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57
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58 .. _RSeQC: http://rseqc.sourceforge.net/
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59
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60 </help>
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61 </tool>