Mercurial > repos > iuc > falco
diff falco.xml @ 4:959a14c1f2dd draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit a71120623d1dc818a107ca32f2c232fd47d819ea
| author | iuc |
|---|---|
| date | Fri, 27 Sep 2024 17:41:40 +0000 |
| parents | babbcf02d35c |
| children |
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--- a/falco.xml Tue Sep 10 19:02:42 2024 +0000 +++ b/falco.xml Fri Sep 27 17:41:40 2024 +0000 @@ -1,7 +1,7 @@ <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> @@ -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="<html><head>.+<title> 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="<html><head>.+<title> 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="<html><head>.+<title> 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="<html><head>.+<title> 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="<html><head>.+<title> 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="<html><head>.+<title> 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="<html><head>.+<title> 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"> @@ -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="<html><head>.+<title> 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="<html><head>.+<title> 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="<html><head>.+<title> 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="<html><head>.+<title> 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[ @@ -159,15 +221,15 @@ 💚️ 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 @@ -181,13 +243,10 @@ 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. +- you need the HTML report to be viewable offline -- your input consists of *mapped* reads in SAM/BAM format - - 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. -----