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annotate inner_distance.xml @ 7:d06c7d4fdc29 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit a63ead9b3f0c781032beabf8bed2c65445500291
author iuc
date Tue, 18 Sep 2018 05:21:29 -0400
parents 017eaaf58e5e
children ef10815e91b3
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1 <tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_VERSION@.1">
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2 <description>calculate the inner distance (or insert size) between two paired RNA reads</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 <expand macro="requirements" />
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[inner_distance.py --version]]></version_command>
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14 <command><![CDATA[
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15 inner_distance.py -i '${input}' -o output -r '${refgene}'
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16 --sample-size ${sample_size}
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17 --lower-bound ${lowerBound}
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18 --upper-bound ${upperBound}
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19 --step ${step}
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20 --mapq ${mapq}
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21 ]]>
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22 </command>
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23
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24 <inputs>
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25 <expand macro="bam_sam_param" />
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26 <expand macro="refgene_param" />
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27 <expand macro="sample_size_param" />
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28 <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/>
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29 <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/>
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30 <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/>
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31 <expand macro="mapq_param" />
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32 <expand macro="rscript_output_param" />
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33 </inputs>
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34
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35 <outputs>
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36 <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" />
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37 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (text)"/>
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38 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (frequency text)" />
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39 <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" />
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40 </outputs>
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41
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42 <tests>
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43 <test>
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44 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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45 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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46 <param name="rscript_output" value="true" />
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47 <output name="outputtxt" file="output.inner_distance.txt" />
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48 <output name="outputfreqtxt" file="output.inner_distance_freq.txt" />
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49 <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/>
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50 <output name="outputr" file="output.inner_distance_plot.r" />
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51 </test>
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52 </tests>
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53
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54 <help><![CDATA[
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55 inner_distance.py
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56 +++++++++++++++++
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58 This module is used to calculate the inner distance (or insert size) between two paired RNA
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59 reads. The distance is the mRNA length between two paired fragments. We first determine the
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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60 genomic (DNA) size between two paired reads: D_size = read2_start - read1_end, then
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61
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62 * if two paired reads map to the same exon: inner distance = D_size
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63 * if two paired reads map to different exons:inner distance = D_size - intron_size
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64 * if two paired reads map non-exonic region (such as intron and intergenic region): inner distance = D_size
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65 * The inner_distance might be a negative value if two fragments were overlapped.
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66
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67 NOTE: Not all read pairs were used to estimate the inner distance distribution. Those low
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68 quality, PCR duplication, multiple mapped reads were skipped.
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70 Inputs
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71 ++++++++++++++
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73 Input BAM/SAM file
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74 Alignment file in BAM/SAM format.
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76 Reference gene model
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77 Gene model in BED format.
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79 Estimated Upper/Lower Bounds (defaults=250 and -250)
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80 Estimated upper/lower bounds of inner distance (bp).
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81
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82 Step size (default=5)
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83 Step size of histogram
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86 Output
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87 ++++++++++++++
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89 1. output.inner_distance.txt:
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90 - first column is read ID
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91 -second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start &lt; Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1)
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92 - third column indicates how paired reads were mapped: PE_within_same_exon, PE_within_diff_exon,PE_reads_overlap
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93 2. output..inner_distance_freq.txt:
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94 - inner distance starts
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95 - inner distance ends
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96 - number of read pairs
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97 - note the first 2 columns are left side half open interval
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98 3. output.inner_distance_plot.r: R script to generate histogram
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99 4. output.inner_distance_plot.pdf: histogram plot
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100
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101 .. image:: $PATH_TO_IMAGES/inner_distance.png
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102 :height: 600 px
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103 :width: 600 px
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104 :scale: 80 %
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105
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106 @ABOUT@
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107
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108 ]]>
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109 </help>
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110
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111 <expand macro="citations" />
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112
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113 </tool>