Mercurial > repos > iuc > qualifilter

annotate qualifilter.xml @ 0:b694fab47ac7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
author iuc
date Mon, 15 Dec 2025 14:04:25 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
1 <tool id="qualifilter" name="QualiFilter" version="@TOOL_VERSION@@VERSION_SUFFIX@" profile="@PROFILE@">
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
2 <description>Report QC metrics and sample pass/fail based on user-defined thresholds</description>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
3
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
4 <macros>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
5 <import>macros.xml</import>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
6 </macros>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
7
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
8 <requirements>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
9 <requirement type="package" version="1.0.0">qualifilter</requirement>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
10 </requirements>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
11
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
12 <version_command>echo @TOOL_VERSION@</version_command>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
13
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
14 <command detect_errors="exit_code" ><![CDATA[
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
15 qualifilter
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
16 --input '$input_file'
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
17 --attributes '$attributes'
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
18 --thresholds "{\"Total_reads\": ${total_reads}, \"Coverage_gte_10x_pct\": ${coverage_gte_10x_pct}, \"Contam_pct\": ${contam_max}}"
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
19 --round '${round}'
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
20 $derive_reads
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
21 #if $config
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
22 --config '$config'
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
23 #end if
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
24 --outdir .
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
25 > qualifilter.log 2>&1
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
26 ]]></command>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
27
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
28 <inputs>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
29 <param name="input_file" type="data" format="tabular" label="Input summary file" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
30
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
31 <param argument="--attributes" type="select" multiple="true" optional="true"
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
32 label="QC metrics to include"
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
33 help="Select which metrics to include in the output. Leave empty to include all.">
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
34 <option value="Sample">Sample</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
35 <option value="Total_reads">Total reads</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
36 <option value="Mapped_reads">Mapped reads</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
37 <option value="Mapping_pct">Mapping %</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
38 <option value="Median_depth">Median depth</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
39 <option value="Coverage_gte_10x_pct">Coverage ≥10x %</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
40 <option value="GC_pct">GC %</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
41 <option value="Kraken_top1_pct">Kraken top1 %</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
42 <option value="Kraken_unclassified_pct">Kraken unclassified %</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
43 <option value="Contam_pct">Contamination %</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
44 <option value="QC_status">QC status</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
45 <option value="Total_reads_pass">Total reads pass</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
46 <option value="Coverage_gte_10x_pct_pass">Coverage at ≥10x pass</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
47 <option value="Contam_pct_pass">Contamination pass</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
48 <option value="MTB_reads">MTB reads</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
49 <option value="Unclassified_reads">Unclassified reads</option>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
50 </param>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
51
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
52 <param name="total_reads" type="float" value="1000000" min="0" label="Minimum total reads" help="Minimum number of sequencing reads required for a sample to pass QC (commonly ≥1M for microbial WGS)." />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
53 <param name="coverage_gte_10x_pct" type="float" value="90" min="0" max="100" label="Minimum coverage pct at ≥10x depth" help="Percentage of the genome covered at ≥10x depth. Values ≥90% are generally considered good quality." />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
54 <param name="contam_max" type="float" value="5" min="0" max="100" label="Maximum contamination %" help="Maximum proportion of reads not belonging to the target organism (typically ≤5%)." />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
55 <param name="round" type="integer" value="2" min="0" label="Rounding precision" help="Number of decimal places used to round numeric values in the output." />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
56
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
57 <param name="config" type="data" format="yaml" optional="true"
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
58 label="Optional config file"
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
59 help="Provide a YAML or JSON config file to override default allowed columns and rename map. Only advanced users need this." />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
60
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
61 <param argument="--derive_reads" type="boolean"
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
62 truevalue="--derive_reads" falsevalue=""
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
63 label="Derive MTB/unclassified reads" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
64 </inputs>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
65
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
66 <outputs>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
67 <data name="qc_matrix_tsv" format="tsv" label="QC Matrix (TSV)" from_work_dir="QC_matrix.tsv" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
68 <data name="qc_matrix_csv" format="csv" label="QC Matrix (CSV)" from_work_dir="QC_matrix.csv" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
69 <data name="log" format="txt" label="QualiFilter Log" from_work_dir="qualifilter.log" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
70 </outputs>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
71
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
72 <tests>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
73 <test expect_num_outputs="3">
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
74 <param name="input_file" value="qc_matrix.tabular" ftype="tabular"/>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
75 <param name="attributes" value="Sample,Total_reads,Mapped_reads,Mapping_pct,Median_depth,Coverage_gte_10x_pct,GC_pct,Kraken_top1_pct,Kraken_unclassified_pct,Contam_pct,QC_status,Total_reads_pass,Coverage_gte_10x_pct_pass,Contam_pct_pass,MTB_reads,Unclassified_reads" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
76 <param name="total_reads" value="1000000" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
77 <param name="coverage_gte_10x_pct" value="90" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
78 <param name="contam_max" value="5" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
79 <param name="round" value="2" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
80 <param name="derive_reads" value="true" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
81
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
82 <output name="qc_matrix_tsv" file="QC_matrix.tsv" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
83 <output name="qc_matrix_csv" file="QC_matrix.csv" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
84 <output name="log" file="qualifilter.log" />
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
85 </test>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
86 </tests>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
87
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
88 <help><![CDATA[
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
89 **What it does**
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
90
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
91 This tool extracts sequencing quality control (QC) metrics from a MultiQC tabular summary (.tabular) file and generates a consolidated QC matrix containing only the metrics of interest.
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
92 It summarizes key metrics including Total reads, Mapped reads, Coverage percentage, and Contamination.
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
93 Each sample is automatically evaluated against user-defined QC thresholds (provided as a JSON string) to assign a QC Pass/Fail status.
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
94
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
95 **Input**
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
96 - A MultiQC-generated .tabular file containing per-sample QC metrics
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
97 - User-defined thresholds for Total reads, Coverage >=10x percentage, Maximum contamination percentage
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
98 - You can specify which QC metrics to include in the output using the --attributes option (comma-separated list). If left empty, all available metrics will be included automatically
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
99 - Optionally, a YAML or JSON config file can be provided to customize allowed columns and rename mappings
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
100
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
101 **Available metrics / attributes**
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
102 - Sample - unique identifier for each sample
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
103 - Total_reads - total number of sequencing reads
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
104 - Mapped_reads - reads mapped to the reference genome
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
105 - Median_depth - median sequencing coverage across the genome
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
106 - Coverage_gte_10x_pct - percentage of the genome covered at >=10x depth
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
107 - GC_pct - GC content percentage of reads
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
108 - Kraken_top1_pct - percentage of reads assigned to the top taxonomic hit by Kraken
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
109 - Kraken_unclassified_pct - percentage of reads unclassified by Kraken
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
110 - Contam_pct - estimated contamination percentage
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
111 - QC_status - Pass/Fail status of the sample based on thresholds
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
112 - MTB_reads (optional, derived if --derive_reads is selected) - reads assigned to the target organism
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
113 - Unclassified_reads (optional, derived if --derive_reads is selected) - reads that could not be classified
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
114
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
115 **Output**
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
116 - A summarized QC matrix in TSV format
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
117 - A summarized QC matrix in CSV format
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
118 - Both outputs include Pass/Fail status for each sample based on the threshold evaluation
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
119
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
120 **Threshold behavior**
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
121 - Thresholds are provided as a JSON-formatted string. Example: {"Total_reads": 1000000, "Coverage_gte_10x_pct": 90, "Contam_pct": 5}
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
122
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
123 **Optional configuration file**
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
124
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
125 - An optional YAML or JSON configuration file can be supplied for advanced use cases where the default behavior needs to be customized. This file allows users to:
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
126 - Define custom allowed columns
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
127 - Rename columns in the output matrix
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
128
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
129 Example YAML::
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
130
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
131 allowed_columns:
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
132 - Sample
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
133 - Total_reads
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
134 - Coverage_gte_10x_pct
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
135 - Contam_pct
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
136
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
137 rename_map:
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
138 qualimap_bamqc-total_reads: Total_reads
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
139 qualimap_bamqc-mapped_reads: Mapped_reads
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
140 qualimap_bamqc-percentage_aligned: Mapping_pct
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
141 qualimap_bamqc-median_coverage: Median_depth
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
142
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
143 **Additional Notes**
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
144 - Read count fields (Total_reads, Mapped_reads) are automatically scaled if MultiQC reports them in millions (e.g., Qualimap output). No action is required
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
145 - If no QC metric attributes are selected, the tool includes all available columns
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
146 - Derived read metrics (MTB_reads, Unclassified_reads) are calculated only when the relevant option is enabled
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
147 - Default thresholds: Total reads >= 1000000, Coverage >=10x percentage >= 90, Contamination percentage <= 5
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
148 - Rounding precision for numeric metrics can be adjusted (default is 2 decimal places)
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
149 - The tool generates a log file documenting the processing steps and any issues encountered
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
150
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
151 ]]></help>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
152
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
153 <citations>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
154 <citation type="bibtex">
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
155 @misc{bntozini2025,
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
156 author = {Buhle Ntozini},
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
157 year = {2025},
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
158 title = {QualiFilter: QC matrix extractor and decision tool},
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
159 publisher = {GitHub},
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
160 journal = {GitHub repository},
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
161 url = {https://github.com/buhlentozini/QualiFilter}
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
162 }
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
163 </citation>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
164 </citations>
b694fab47ac7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter commit c1d08b00ccb4837dd592970d2000f5fffe695e9f
iuc
parents:
diff changeset
165 </tool>