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annotate infer_experiment.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
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1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>speculates how RNA-seq were configured</description>
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3 <macros>
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4 <import>rseqc_macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <version_command><![CDATA[infer_experiment.py --version]]></version_command>
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10 <command><![CDATA[
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11 @BAM_SAM_INPUTS@
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12 infer_experiment.py -i 'input.${extension}' -r '${refgene}'
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13 --sample-size ${sample_size}
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14 --mapq ${mapq}
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15 > '${output}'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="bam_param"/>
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20 <expand macro="refgene_param"/>
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21 <expand macro="sample_size_param"/>
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22 <expand macro="mapq_param"/>
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23 </inputs>
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24 <outputs>
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25 <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration"/>
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26 </outputs>
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27 <tests>
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28 <test expect_num_outputs="1">
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29 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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30 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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31 <output name="output" file="output.infer_experiment.txt"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 infer_experiment.py
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36 +++++++++++++++++++
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37
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38 This program is used to speculate how RNA-seq sequencing were configured, especially how
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39 reads were stranded for strand-specific RNA-seq data, through comparing reads' mapping
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40 information to the underneath gene model.
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43 Inputs
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44 ++++++++++++++
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45
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46 Input BAM/SAM file
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47 Alignment file in BAM/SAM format.
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48
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49 Reference gene model
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50 Gene model in BED format.
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51
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52 Number of usable sampled reads (default=200000)
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53 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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54
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55 Outputs
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56 +++++++
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57
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58 For pair-end RNA-seq, there are two different
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59 ways to strand reads (such as Illumina ScriptSeq protocol):
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60
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61 1. 1++,1--,2+-,2-+
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62
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63 * read1 mapped to '+' strand indicates parental gene on '+' strand
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64 * read1 mapped to '-' strand indicates parental gene on '-' strand
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65 * read2 mapped to '+' strand indicates parental gene on '-' strand
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66 * read2 mapped to '-' strand indicates parental gene on '+' strand
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67
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68 2. 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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74
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75 For single-end RNA-seq, there are also two different ways to strand reads:
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76
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77 1. ++,--
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78
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79 * read mapped to '+' strand indicates parental gene on '+' strand
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80 * read mapped to '-' strand indicates parental gene on '-' strand
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81
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82 2. +-,-+
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83
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84 * read mapped to '+' strand indicates parental gene on '-' strand
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85 * read mapped to '-' strand indicates parental gene on '+' strand
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86
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87
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88 Example Output
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89 ++++++++++++++
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90
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91 **Example1** ::
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92
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93 =========================================================
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94 This is PairEnd Data ::
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95
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96 Fraction of reads explained by "1++,1--,2+-,2-+": 0.4992
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97 Fraction of reads explained by "1+-,1-+,2++,2--": 0.5008
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98 Fraction of reads explained by other combinations: 0.0000
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99 =========================================================
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100
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101 *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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102
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103 **Example2** ::
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104
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105 ============================================================
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106 This is PairEnd Data
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107
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108 Fraction of reads explained by "1++,1--,2+-,2-+": 0.9644 ::
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109 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0356
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110 Fraction of reads explained by other combinations: 0.0000
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111 ============================================================
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112
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113 *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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114
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115 **Example3** ::
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116
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117 =========================================================
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118 This is SingleEnd Data ::
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119
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120 Fraction of reads explained by "++,--": 0.9840 ::
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121 Fraction of reads explained by "+-,-+": 0.0160
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122 Fraction of reads explained by other combinations: 0.0000
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123 =========================================================
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124
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125 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.
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126
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127 @ABOUT@
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128
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129 ]]>
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130 </help>
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131 <expand macro="citations"/>
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132 </tool>