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Merge branch 'galaxyproject:main' into sniffles
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@fubar2
fubar2 authored Sep 28, 2024
2 parents fd83260 + a711206 commit 642e1d0
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131 changes: 95 additions & 36 deletions tools/falco/falco.xml
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<tool id="falco" name="Falco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
<description>An alternative, more performant implementation of FastQC for high throughput sequence quality control</description>
<macros>
<token name="@TOOL_VERSION@">1.2.3</token>
<token name="@TOOL_VERSION@">1.2.4</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<xrefs>
Expand Down Expand Up @@ -74,28 +74,81 @@
</data>
</outputs>
<tests>
<!-- Test with fastq input -->
<test expect_num_outputs="2">
<param name="input_file" value="1000trimmed.fastq"/>
<output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_data.txt" ftype="txt"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<!-- two lines diff to allow for reported version to change -->
<output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
</test>
<!-- Test with fastq.gz input -->
<test expect_num_outputs="2">
<param name="input_file" value="1000trimmed.fastq.gz"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq_gz - report.+"/>
</assert_contents>
</output>
<!-- four lines diff to allow for reported version to change; two more to accomodate changed input file name -->
<output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
</test>
<!-- Test with BAM input -->
<test expect_num_outputs="2">
<param name="input_file" value="hisat_output_1.bam"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; hisat_output_1_bam - report.+"/>
</assert_contents>
</output>
<!-- four lines diff to allow for reported version to change; two more to accomodate changed input file name -->
<output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="4"/>
</test>
<!-- Test summary file option -->
<test expect_num_outputs="3">
<param name="input_file" value="1000trimmed.fastq"/>
<param name="generate_summary" value="true"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
<output name="summary_file" file="fastqc_data_summary.txt" ftype="txt"/>
</test>
<test expect_num_outputs="2">
<param name="input_file" value="1000trimmed.fastq"/>
<param name="contaminants" value="contaminant_list.txt" ftype="tabular"/>
<output name="html_file" file="fastqc_report_contaminants.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt" lines_diff="2"/>
</test>
<test expect_num_outputs="2">
<param name="input_file" value="1000trimmed.fastq"/>
<param name="adapters" value="adapter_list.txt" ftype="tabular"/>
<output name="html_file" file="fastqc_report_adapters.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="text_file" file="fastqc_data_adapters.txt" ftype="txt" lines_diff="2"/>
</test>
<test expect_num_outputs="2">
<test expect_num_outputs="3">
<param name="input_file" value="1000trimmed.fastq"/>
<param name="limits" value="limits.txt" ftype="txt"/>
<output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/>
<param name="generate_summary" value="true"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="summary_file" file="fastqc_data_customlimits_summary.txt" ftype="txt"/>
</test>
<!-- ## The kmers param is ignored in Falco and always set to 7. If this ever gets reconsidered, this test could be uncommented.
<test expect_num_outputs="2">
Expand All @@ -116,40 +169,49 @@
<output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/>
</test> -->
<test expect_num_outputs="3">
<test expect_num_outputs="2">
<param name="input_file" value="1000trimmed.fastq" ftype="fastq"/>
<param name="nogroup" value="--nogroup"/>
<param name="generate_summary" value="true"/>
<output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/>
<output name="summary_file" file="fastqc_data_nogroup_summary.txt" ftype="txt"/>
<assert_command>
<has_text text="--nogroup"/>
</assert_command>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt" lines_diff="2"/>
</test>
<test expect_num_outputs="3">
<param name="input_file" value="1000trimmed.fastq"/>
<param name="subsample" value="10"/>
<param name="generate_summary" value="true"/>
<output name="html_file" file="fastqc_report_subsample.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_report_subsample.txt" ftype="txt"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="text_file" file="fastqc_report_subsample.txt" ftype="txt" lines_diff="2"/>
<output name="summary_file" file="fastqc_report_subsample_summary.txt" ftype="txt"/>
</test>
<test expect_num_outputs="3">
<param name="input_file" value="1000trimmed.fastq"/>
<param name="bisulfite" value="-bisulfite"/>
<param name="generate_summary" value="true"/>
<output name="html_file" file="fastqc_report_bisulfite.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt" lines_diff="2"/>
<output name="summary_file" file="fastqc_report_bisulfite_summary.txt" ftype="txt"/>
</test>
<test expect_num_outputs="3">
<test expect_num_outputs="2">
<param name="input_file" value="1000trimmed.fastq"/>
<param name="reverse_complement" value="-reverse-complement"/>
<param name="generate_summary" value="true"/>
<output name="html_file" file="fastqc_report_reverse_complement.html" ftype="html" lines_diff="2"/>
<output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt"/>
<output name="summary_file" file="fastqc_report_reverse_complement_summary.txt" ftype="txt"/>
<output name="html_file" ftype="html">
<assert_contents>
<has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
</assert_contents>
</output>
<output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt" lines_diff="2"/>
</test>
</tests>
<help><![CDATA[
Expand All @@ -159,15 +221,15 @@ Falco_ is a high-speed emulation of the popular FastQC software for quality cont
💚️ With its superior performance Falco saves computational resources and gives you back results faster than FastQC.
We recommend it for most use cases (but see below for exceptions). 💚️
We recommend it for most use cases (but see below for rare exceptions). 💚️
The main functions of Falco are very similar to those of FastQC:
- Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application
- Export of results to an HTML-based report
.. class:: infomark
Expand All @@ -181,13 +243,10 @@ The plain text report generated by Falco can be used as a "FastQC" report in Mul
Falco doesn't currently support fastq.bz2 as input format meaning Galaxy has to perform a relatively slow format conversion before running the tool, which together makes the analysis slower than with FastQC.
- you are interested in PolyA and PolyG statistics in the Adapter Content section of the quality report
Falco doesn't currently calculate statistics for these "Adapters" by default.
- your input consists of *mapped* reads in SAM/BAM format
- you need the HTML report to be viewable offline
Due to a bug in the current version of Falco, reads mapped to the reverse strand of the reference genome are not handled correctly and reported metrics are wrong!
The current version of Falco relies on plotly to generate the graphs in the HTML report dynamically each time it's viewed.
MultiQC plots generated from Falco's raw data output are, of course, viewable offline just like the ones generated from FastQC output.
-----
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