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annotate infer_experiment.xml @ 9:ef10815e91b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7d7cd4324af66710b89801a1a1c79fb8abf0d146
author iuc
date Thu, 27 Sep 2018 14:23:25 -0400
parents 017eaaf58e5e
children d7f6b3653d84
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1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@.1">
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2 <description>speculates how RNA-seq were configured</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[infer_experiment.py --version]]></version_command>
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14 <command><![CDATA[
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15 infer_experiment.py -i '${input}' -r '${refgene}'
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16 --sample-size ${sample_size}
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17 --mapq ${mapq}
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18 > '${output}'
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19 ]]>
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20 </command>
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21
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22 <inputs>
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23 <expand macro="bam_param" />
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24 <expand macro="refgene_param" />
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25 <expand macro="sample_size_param" />
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26 <expand macro="mapq_param" />
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27 </inputs>
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29 <outputs>
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30 <data format="txt" name="output" />
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31 </outputs>
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32
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33 <tests>
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34 <test>
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35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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36 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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37 <output name="output" file="output.infer_experiment.txt"/>
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38 </test>
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39 </tests>
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40
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41 <help><![CDATA[
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42 infer_experiment.py
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43 +++++++++++++++++++
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44
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45 This program is used to speculate how RNA-seq sequencing were configured, especially how
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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46 reads were stranded for strand-specific RNA-seq data, through comparing reads' mapping
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47 information to the underneath gene model.
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50 Inputs
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51 ++++++++++++++
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52
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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 Reference gene model
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57 Gene model in BED format.
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58
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59 Number of usable sampled reads (default=200000)
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60 Number of usable reads sampled from SAM/BAM file. More reads will give more accurate estimation, but make program little slower.
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61
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62 Outputs
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63 +++++++
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64
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65 For pair-end RNA-seq, there are two different
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66 ways to strand reads (such as Illumina ScriptSeq protocol):
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67
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68 1. 1++,1--,2+-,2-+
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69
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70 * read1 mapped to '+' strand indicates parental gene on '+' strand
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71 * read1 mapped to '-' strand indicates parental gene on '-' strand
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72 * read2 mapped to '+' strand indicates parental gene on '-' strand
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73 * read2 mapped to '-' strand indicates parental gene on '+' strand
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75 2. 1+-,1-+,2++,2--
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77 * read1 mapped to '+' strand indicates parental gene on '-' strand
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78 * read1 mapped to '-' strand indicates parental gene on '+' strand
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79 * read2 mapped to '+' strand indicates parental gene on '+' strand
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80 * read2 mapped to '-' strand indicates parental gene on '-' strand
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81
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82 For single-end RNA-seq, there are also two different ways to strand reads:
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83
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84 1. ++,--
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86 * read mapped to '+' strand indicates parental gene on '+' strand
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87 * read mapped to '-' strand indicates parental gene on '-' strand
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89 2. +-,-+
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91 * read mapped to '+' strand indicates parental gene on '-' strand
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92 * read mapped to '-' strand indicates parental gene on '+' strand
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93
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94
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95 Example Output
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96 ++++++++++++++
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97
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98 **Example1** ::
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99
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100 =========================================================
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101 This is PairEnd Data ::
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102
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103 Fraction of reads explained by "1++,1--,2+-,2-+": 0.4992
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104 Fraction of reads explained by "1+-,1-+,2++,2--": 0.5008
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105 Fraction of reads explained by other combinations: 0.0000
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106 =========================================================
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107
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108 *Conclusion*: We can infer that this is NOT a strand specific because 50% of reads can be explained by "1++,1--,2+-,2-+", while the other 50% can be explained by "1+-,1-+,2++,2--".
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109
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110 **Example2** ::
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111
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112 ============================================================
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113 This is PairEnd Data
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114
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115 Fraction of reads explained by "1++,1--,2+-,2-+": 0.9644 ::
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116 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0356
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117 Fraction of reads explained by other combinations: 0.0000
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118 ============================================================
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119
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120 *Conclusion*: We can infer that this is a strand-specific RNA-seq data. strandness of read1 is consistent with that of gene model, while strandness of read2 is opposite to the strand of reference gene model.
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121
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122 **Example3** ::
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123
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124 =========================================================
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125 This is SingleEnd Data ::
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126
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127 Fraction of reads explained by "++,--": 0.9840 ::
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128 Fraction of reads explained by "+-,-+": 0.0160
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129 Fraction of reads explained by other combinations: 0.0000
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130 =========================================================
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131
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132 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.
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133
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134 @ABOUT@
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135
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136 ]]>
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137 </help>
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138
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139 <expand macro="citations" />
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140
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141 </tool>