Mercurial > repos > lparsons > rseqc

annotate clipping_profile.xml @ 1:cd2daa987b69 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
author lparsons
date Tue, 07 Jul 2015 14:14:04 -0400
parents 306127635959
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.4galaxy1">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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2 <description>
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3 estimates clipping profile of RNA-seq reads from BAM or SAM file
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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4 </description>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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10 <requirements>
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11 <expand macro="requirement_package_r" />
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12 <expand macro="requirement_package_numpy" />
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13 <expand macro="requirement_package_rseqc" />
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14 </requirements>
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16 <expand macro="stdio" />
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18 <version_command><![CDATA[clipping_profile.py --version]]></version_command>
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20 <command><![CDATA[
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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21 clipping_profile.py -i $input -o output
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22 ]]>
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23 </command>
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25 <inputs>
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cd2daa987b69 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
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26 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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27 </inputs>
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29 <outputs>
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30 <data format="pdf" name="outputpdf" from_work_dir="output.clipping_profile.pdf" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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31 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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32 <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
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33 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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38 <output name="outputpdf" file="output.clipping_profile.pdf"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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39 <output name="outputxls" file="output.clipping_profile.xls"/>
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40 <output name="outputr" file="output.clipping_profile.r"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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41 </test>
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42 </tests>
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44 <help><![CDATA[
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45 clipping_profile.py
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46 +++++++++++++++++++
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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48 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
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49 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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50 (This means your reads aligner should support clipped mapping).
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52 Inputs
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53 ++++++++++++++
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54
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55 Input BAM/SAM file
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56 Alignment file in BAM/SAM format.
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59 Sample Output
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60 ++++++++++++++
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62 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
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63 :height: 600 px
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64 :width: 600 px
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65 :scale: 80 %
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67 -----
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69 About RSeQC
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70 +++++++++++
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72 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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74 The RSeQC package is licensed under the GNU GPL v3 license.
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76 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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78 .. _RSeQC: http://rseqc.sourceforge.net/
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79 ]]>
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80 </help>
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82 <expand macro="citations" />
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84 </tool>