Mercurial > repos > iuc > ngsderive_strandedness

annotate ngsderive_strandedness.xml @ 0:bb8409cb3005 draft default tip

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author iuc
date Fri, 09 Jan 2026 09:57:07 +0000
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0
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1 <tool id="ngsderive_strandedness" name="ngsderive strandedness" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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2 <description>infers strandedness from RNA-seq BAM files</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">4.0.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">ngsderive</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '${alignment_input}' input.bam &&
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12 ln -s '${alignment_input.metadata.bam_index}' input.bam.bai &&
bb8409cb3005 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsderive commit 431830f24865316ab81526f053c171abf9f09529
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13 ln -s '${gtf_input}' annotation.${gtf_input.ext} &&
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14
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15 ngsderive strandedness
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16 input.bam
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17 -g annotation.${gtf_input.ext}
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18 -n $n_genes
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19 -m $min_reads_per_gene
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20 -q $mapq
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21 $split_by_rg
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22 > '${output}'
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23 ]]></command>
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24 <inputs>
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25 <param name="alignment_input" type="data" format="bam" label="Input alignment file" help="Aligned paired-end RNA-seq reads in BAM format."/>
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26 <param name="gtf_input" type="data" format="gtf,gtf.gz" label="Gene annotation file (GTF)" help="Gene model in GTF format. The file will be automatically sorted and indexed if necessary."/>
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27 <param argument="-n" name="n_genes" type="integer" value="1000" min="1" label="Number of genes to sample" help="Number of random genes to sample for strandedness inference."/>
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28 <param argument="-m" name="min_reads_per_gene" type="integer" value="10" min="1" label="Minimum reads per gene" help="Minimum number of reads per gene required for inclusion in the analysis."/>
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29 <param argument="-q" name="mapq" type="integer" value="30" min="0" label="Minimum mapping quality (MAPQ)" help="Minimum MAPQ score for a read to be considered."/>
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30 <param argument="--split-by-rg" type="boolean" truevalue="--split-by-rg" falsevalue="" checked="false" label="Split results by read group" help="Output one entry per read group in addition to an overall entry."/>
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31 </inputs>
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32 <outputs>
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33 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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34 <actions>
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35 <action name="column_names" type="metadata" default="File,ReadGroup,TotalReads,ForwardPct,ReversePct,Predicted"/>
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36 </actions>
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37 </data>
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38 </outputs>
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39 <tests>
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40 <!-- Test forward-stranded data -->
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41 <test expect_num_outputs="1">
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42 <param name="alignment_input" value="forward_stranded.bam"/>
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43 <param name="gtf_input" value="strandedness_test.gtf"/>
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44 <output name="output">
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45 <assert_contents>
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46 <has_n_columns n="6"/>
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47 <has_text text="Stranded-Forward"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 <!-- Test reverse-stranded data -->
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52 <test expect_num_outputs="1">
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53 <param name="alignment_input" value="reverse_stranded.bam"/>
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54 <param name="gtf_input" value="strandedness_test.gtf"/>
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55 <output name="output">
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56 <assert_contents>
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57 <has_n_columns n="6"/>
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58 <has_text text="Stranded-Reverse"/>
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59 </assert_contents>
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60 </output>
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61 </test>
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62 <!-- Test unstranded data -->
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63 <test expect_num_outputs="1">
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64 <param name="alignment_input" value="unstranded.bam"/>
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65 <param name="gtf_input" value="strandedness_test.gtf"/>
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66 <output name="output">
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67 <assert_contents>
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68 <has_n_columns n="6"/>
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69 <has_text text="Unstranded"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 <!-- Test with gzipped GTF annotation file -->
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74 <test expect_num_outputs="1">
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75 <param name="alignment_input" value="reverse_stranded.bam"/>
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76 <param name="gtf_input" value="strandedness_test.gtf.gz" ftype="gtf.gz"/>
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77 <output name="output">
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78 <assert_contents>
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79 <has_n_columns n="6"/>
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80 <has_text text="Stranded-Reverse"/>
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81 </assert_contents>
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82 </output>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86 **What it does**
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87
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88 ngsderive strandedness infers the strandedness protocol used to generate RNA-seq data by
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89 analyzing read alignments against a gene model. It can determine whether your data was
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90 generated using a Stranded-Forward, Stranded-Reverse, or Unstranded protocol.
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91
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92 This tool is useful when you have RNA-seq data but are unsure about the library preparation
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93 protocol used. Knowing the correct strandedness is essential for accurate gene expression
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94 quantification.
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95
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96 **How it works**
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97
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98 The tool randomly samples genes from the provided gene model and examines how reads align
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99 to those genes. Based on the proportion of reads mapping in the forward vs reverse orientation,
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100 it classifies the library as:
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101
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102 - **Unstranded**: ~40-60% forward reads
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103 - **Stranded-Forward**: ≥80% forward reads
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104 - **Stranded-Reverse**: ≥80% reverse reads
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105 - **Inconclusive**: Results don't clearly indicate a strandedness type
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106
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107 **Inputs**
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108
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109 - **Alignment file**: Paired-end RNA-seq alignments in BAM format
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110 - **Gene annotation**: GTF file with gene models (gzipped GTF supported)
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111
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112 **Output**
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113
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114 A tabular file with the following columns:
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115
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116 - **File**: Name of the input BAM file
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117 - **ReadGroup**: Read group identifier (or "overall" for combined results)
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118 - **TotalReads**: Number of reads used in the analysis
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119 - **ForwardPct**: Percentage of reads supporting forward strandedness
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120 - **ReversePct**: Percentage of reads supporting reverse strandedness
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121 - **Predicted**: The inferred strandedness (Stranded-Forward, Stranded-Reverse, Unstranded, or Inconclusive)
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122
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123 **Notes**
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124
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125 - Only paired-end reads are currently supported
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126 - For best results, ensure your BAM file has sufficient read depth
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127
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128 For more information, see the `ngsderive documentation <https://stjudecloud.github.io/ngsderive/subcommands/strandedness/>`_.
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129 ]]></help>
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130 <citations>
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131 <citation type="bibtex">
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132 @software{ngsderive,
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133 author = {{St. Jude Cloud Team}},
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134 title = {ngsderive: Forensic analysis tool for NGS data},
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135 url = {https://github.com/stjudecloud/ngsderive},
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136 year = {2020}
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137 }
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138 </citation>
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139 </citations>
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140 </tool>