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annotate infer_experiment.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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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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7 <expand macro="bio_tools"/>
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9 <expand macro="requirements" />
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11 <expand macro="stdio" />
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13 <version_command><![CDATA[infer_experiment.py --version]]></version_command>
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15 <command><![CDATA[
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16 @BAM_SAM_INPUTS@
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17 infer_experiment.py -i 'input.${extension}' -r '${refgene}'
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18 --sample-size ${sample_size}
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19 --mapq ${mapq}
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20 > '${output}'
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21 ]]>
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22 </command>
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24 <inputs>
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25 <expand macro="bam_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 <expand macro="mapq_param" />
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29 </inputs>
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31 <outputs>
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32 <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration" />
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33 </outputs>
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34
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35 <tests>
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36 <test>
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37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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38 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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39 <output name="output" file="output.infer_experiment.txt"/>
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40 </test>
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41 </tests>
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43 <help><![CDATA[
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44 infer_experiment.py
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45 +++++++++++++++++++
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47 This program is used to speculate how RNA-seq sequencing were configured, especially how
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48 reads were stranded for strand-specific RNA-seq data, through comparing reads' mapping
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49 information to the underneath gene model.
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52 Inputs
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53 ++++++++++++++
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55 Input BAM/SAM file
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56 Alignment file in BAM/SAM format.
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58 Reference gene model
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59 Gene model in BED format.
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60
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61 Number of usable sampled reads (default=200000)
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62 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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63
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64 Outputs
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65 +++++++
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67 For pair-end RNA-seq, there are two different
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68 ways to strand reads (such as Illumina ScriptSeq protocol):
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70 1. 1++,1--,2+-,2-+
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72 * read1 mapped to '+' strand indicates parental gene on '+' strand
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73 * read1 mapped to '-' strand indicates parental gene on '-' strand
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74 * read2 mapped to '+' strand indicates parental gene on '-' strand
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75 * read2 mapped to '-' strand indicates parental gene on '+' strand
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77 2. 1+-,1-+,2++,2--
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79 * read1 mapped to '+' strand indicates parental gene on '-' strand
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80 * read1 mapped to '-' strand indicates parental gene on '+' strand
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81 * read2 mapped to '+' strand indicates parental gene on '+' strand
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82 * read2 mapped to '-' strand indicates parental gene on '-' strand
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84 For single-end RNA-seq, there are also two different ways to strand reads:
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85
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86 1. ++,--
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88 * read mapped to '+' strand indicates parental gene on '+' strand
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89 * read mapped to '-' strand indicates parental gene on '-' strand
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91 2. +-,-+
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93 * read mapped to '+' strand indicates parental gene on '-' strand
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94 * read mapped to '-' strand indicates parental gene on '+' strand
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97 Example Output
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98 ++++++++++++++
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99
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100 **Example1** ::
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101
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102 =========================================================
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103 This is PairEnd Data ::
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104
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105 Fraction of reads explained by "1++,1--,2+-,2-+": 0.4992
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106 Fraction of reads explained by "1+-,1-+,2++,2--": 0.5008
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107 Fraction of reads explained by other combinations: 0.0000
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108 =========================================================
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109
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110 *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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111
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112 **Example2** ::
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113
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114 ============================================================
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115 This is PairEnd Data
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116
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117 Fraction of reads explained by "1++,1--,2+-,2-+": 0.9644 ::
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118 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0356
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119 Fraction of reads explained by other combinations: 0.0000
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120 ============================================================
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121
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122 *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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123
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124 **Example3** ::
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125
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126 =========================================================
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127 This is SingleEnd Data ::
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128
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129 Fraction of reads explained by "++,--": 0.9840 ::
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130 Fraction of reads explained by "+-,-+": 0.0160
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131 Fraction of reads explained by other combinations: 0.0000
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132 =========================================================
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133
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134 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.
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135
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136 @ABOUT@
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137
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138 ]]>
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139 </help>
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140
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141 <expand macro="citations" />
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142
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143 </tool>