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Add kat_hist (#1903)
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‎tools/kat/kat_hist.xml‎

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<tool id="kat_hist" name="KAT Histogram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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<description>creates a histogram of k-mer occurrences</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="xrefs"/>
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<expand macro="requirements"/>
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<stdio>
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<regex match="corrupted double-linked list" source="stderr" level="warning" description="KAT C++ heap corruption - output files were still produced correctly"/>
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<exit_code range="2:133" level="fatal" description="Error occurred"/>
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<exit_code range="135:" level="fatal" description="Error occurred"/>
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<exit_code range=":-1" level="fatal" description="Error occurred"/>
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</stdio>
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<version_command>echo @TOOL_VERSION@</version_command>
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<command><![CDATA[
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#for $i in range(len($input_files)):
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#set $f = $input_files[$i]
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@SET_EXT@
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cp '$f' 'input_${i}${ext}' &&
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#end for
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kat hist
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-o kat_hist_out
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-t "\${GALAXY_SLOTS:-1}"
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--low $histogram_options.low
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--high $histogram_options.high
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--inc $histogram_options.inc
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--mer_len $kmer_options.mer_len
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--hash_size $kmer_options.hash_size
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$kmer_options.non_canonical
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@CMD_5PTRIM@
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--output_type '$advanced_options.output_type'
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#for $i in range(len($input_files)):
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#set $f = $input_files[$i]
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@SET_EXT@
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'input_${i}${ext}'
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#end for
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]]></command>
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<inputs>
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<param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" multiple="true" label="Input files" help="One or more FastA/FastQ files (gzipped accepted), or a single Jellyfish hash file"/>
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<section name="histogram_options" title="Histogram Options" expanded="true">
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<param argument="--low" type="integer" value="1" min="1" label="Low count" help="Low count value of histogram"/>
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<param argument="--high" type="integer" value="10000" min="1" label="High count" help="High count value of histogram"/>
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<param argument="--inc" type="integer" value="1" min="1" label="Increment" help="Increment for each bin"/>
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</section>
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<expand macro="kmer_params"/>
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<section name="advanced_options" title="Advanced Options" expanded="false">
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<param name="trim_5p" argument="--5ptrim" type="text" value="" label="5' trim" help="Ignore the first X bases from reads. For multiple input files, provide comma-separated values (e.g. 5,10,0).">
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<validator type="regex" message="Must be a number or comma-separated numbers">^[0-9]+(,[0-9]+)*$|^$</validator>
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</param>
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<expand macro="output_type_param"/>
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</section>
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</inputs>
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<outputs>
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<data name="output_hist" format="tabular" from_work_dir="kat_hist_out" label="${tool.name} on ${on_string}: Histogram"/>
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<data name="output_plot" format="png" from_work_dir="kat_hist_out.png" label="${tool.name} on ${on_string}: PNG Plot">
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<filter>advanced_options['output_type'] == 'png'</filter>
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</data>
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<data name="output_pdf" format="pdf" from_work_dir="kat_hist_out.pdf" label="${tool.name} on ${on_string}: PDF Plot">
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<filter>advanced_options['output_type'] == 'pdf'</filter>
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</data>
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</outputs>
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<tests>
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<!-- Test 01: Default options with PNG Output -->
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<test expect_num_outputs="2">
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<param name="input_files" location="https://zenodo.org/records/20347489/files/kat-input-subsampled.fastq.gz" ftype="fastqsanger.gz"/>
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<section name="histogram_options">
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<param name="low" value="1"/>
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<param name="high" value="10000"/>
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<param name="inc" value="1"/>
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</section>
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<output name="output_hist" file="kat_hist.out">
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<assert_contents>
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<has_text text="# Kmer value:27"/>
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<has_n_lines n="10007"/>
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</assert_contents>
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</output>
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<output name="output_plot" file="kat_hist.out.png" ftype="png">
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<assert_contents>
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<has_image_channels channels="4"/>
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<has_image_height height="1800"/>
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<has_image_width width="2400"/>
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</assert_contents>
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</output>
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</test>
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<!-- Test 02: Custom k-mer length with PDF Output -->
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<test expect_num_outputs="2">
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<param name="input_files" location="https://zenodo.org/records/20347489/files/kat-input-subsampled.fastq.gz" ftype="fastqsanger.gz"/>
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<section name="kmer_options">
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<param name="mer_len" value="21"/>
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</section>
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<section name="advanced_options">
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<param name="output_type" value="pdf"/>
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</section>
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<output name="output_hist">
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<assert_contents>
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<has_text text="# Kmer value:21"/>
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<has_n_lines n="10007"/>
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</assert_contents>
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</output>
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<output name="output_pdf" ftype="pdf">
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<assert_contents>
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<has_size size="13956"/>
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</assert_contents>
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</output>
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</test>
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<!-- Test 03: 5' trim with PNG Output -->
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<test expect_num_outputs="2">
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<param name="input_files" location="https://zenodo.org/records/20347489/files/kat-input-subsampled.fastq.gz" ftype="fastqsanger.gz"/>
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<section name="advanced_options">
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<param name="trim_5p" value="5"/>
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</section>
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<output name="output_hist">
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<assert_contents>
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<has_text text="# Kmer value:27"/>
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<has_n_lines n="10007"/>
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</assert_contents>
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</output>
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<output name="output_plot" ftype="png">
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<assert_contents>
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<has_image_channels channels="4"/>
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<has_image_height height="1800"/>
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<has_image_width width="2400"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help format="markdown"><![CDATA[
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**KAT Histogram (kat hist)**
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Creates a histogram of k-mer occurrences from sequencing data.
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-----
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**What it does**
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The histogram shows how many k-mers appear at each frequency in the input data. Bucket *i* tallies k-mers with count *c* satisfying:
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```
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low + i*inc <= c < low + (i+1)*inc
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```
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The final bucket catches all k-mers with count >= the last bucket's lower bound.
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This tool is similar to the `histo` command in Jellyfish, but the output includes metadata that makes the histogram easier to plot and interpret.
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-----
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**Input**
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- One or more **FASTA** or **FASTQ** files (gzipped accepted)
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- Or a single pre-computed **Jellyfish hash** file
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-----
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**Outputs**
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1. **Histogram** (tabular) - tab-separated count/frequency table with metadata header lines prefixed with `#`.
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2. **Plot** (PNG/PDF) - visual plot of the k-mer frequency histogram.
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-----
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**Tips**
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- The default k-mer length of **27** works well for most short-read sequencing data.
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- For diploid or polyploid genomes, distinct peaks correspond to heterozygous and homozygous k-mers.
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- If the hash size is too small, KAT will automatically double it (increasing runtime and memory). Increase it if you expect many unique k-mers.
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- For multiple input files, provide different 5' trim values as comma-separated numbers (e.g. `5,10`).
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]]></help>
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<expand macro="citations"/>
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<expand macro="creator"/>
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</tool>

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