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annotate read_quality.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
parents f242ee103277
children 34e4c586e3c0
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51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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1 <tool id="rseqc_read_quality" name="Read Quality" version="@WRAPPER_VERSION@">
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2 <description>determines Phred quality score</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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7
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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8 <expand macro="requirements" />
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[read_quality.py --version]]></version_command>
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14 <command><![CDATA[
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15 read_quality.py
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16 --input-file '${input}'
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17 --out-prefix output
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18 -r ${reduce}
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19 --mapq ${mapq}
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20 ]]>
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21 </command>
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22
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23 <inputs>
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24 <expand macro="bam_sam_param" />
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25 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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26 <expand macro="mapq_param" />
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27 <expand macro="rscript_output_param" />
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28 </inputs>
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29
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30 <outputs>
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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31 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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32 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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33 <expand macro="rscript_output_data" filename="output.qual.r" />
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
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39 <param name="rscript_output" value="true" />
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40 <output name="outputr" file="output.qual.r"/>
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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41 <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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42 <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" />
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43 </test>
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44 </tests>
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46 <help><![CDATA[
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47 read_quality.py
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48 +++++++++++++++
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49
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50 According to SAM specification, if Q is the character to represent "base calling quality"
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51 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
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52 returns an integer representing the Unicode code point of the character when the argument
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53 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
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54 to measure "reliability" of base-calling, for example, phred quality score of 20 means
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55 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
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56 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
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57 here P is probability that base-calling is wrong.
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58
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59 Inputs
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60 ++++++++++++++
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61
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62 Input BAM/SAM file
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63 Alignment file in BAM/SAM format.
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64
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65 Ignore phred scores less than this number (default=1000)
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66 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'.
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67
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68 Output
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69 ++++++++++++++
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70
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71 1. output.qual.r
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72 2. output.qual.boxplot.pdf
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73 .. image:: $PATH_TO_IMAGES/36mer.qual.plot.png
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74 :height: 600 px
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75 :width: 600 px
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76 :scale: 80 %
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77 3. output.qual.heatmap.pdf
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78 .. image:: $PATH_TO_IMAGES/36mer.qual.heatmap.png
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79 :height: 600 px
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80 :width: 600 px
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81 :scale: 80 %
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83 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
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84
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85 @ABOUT@
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86
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87 ]]>
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88 </help>
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89
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90 <expand macro="citations" />
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91
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92 </tool>