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