Mercurial > repos > lparsons > rseqc

annotate read_GC.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_read_GC" name="Read GC" 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>determines GC% and read count</description>
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4 <macros>
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5 <import>rseqc_macros.xml</import>
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6 </macros>
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8 <requirements>
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9 <expand macro="requirement_package_r" />
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10 <expand macro="requirement_package_numpy" />
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11 <expand macro="requirement_package_rseqc" />
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12 </requirements>
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14 <expand macro="stdio" />
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16 <version_command><![CDATA[read_GC.py --version]]></version_command>
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18 <command><![CDATA[
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19 read_GC.py
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20 --input-file $input
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21 --out-prefix output
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22 --mapq $mapq
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23 ]]>
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24 </command>
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26 <inputs>
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27 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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28 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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29 </inputs>
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31 <outputs>
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32 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/>
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33 <data format="txt" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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34 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
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35 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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40 <output name="outputxls" file="output.GC.xls"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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41 <output name="outputr" file="output.GC_plot.r"/>
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42 </test>
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43 </tests>
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45 <help><![CDATA[
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46 read_GC.py
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47 ++++++++++
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50 Inputs
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51 ++++++++++++++
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53 Input BAM/SAM file
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54 Alignment file in BAM/SAM format.
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56 Output
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57 ++++++++++++++
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58
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59 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
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60 2. output.GC_plot.r: R script to generate pdf file.
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61 3. output.GC_plot.pdf: graphical output generated from R script.
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62
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63 .. image:: http://rseqc.sourceforge.net/_images/read_gc.png
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64 :height: 600 px
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65 :width: 600 px
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66 :scale: 80 %
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68 -----
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70 About RSeQC
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71 +++++++++++
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73 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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75 The RSeQC package is licensed under the GNU GPL v3 license.
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77 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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79 .. _RSeQC: http://rseqc.sourceforge.net/
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80 ]]>
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81 </help>
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83 <expand macro="citations" />
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85 </tool>