Mercurial > repos > jjohnson > fastq_seq_count
view fastq_seq_count.xml @ 0:27c39155d53b draft default tip
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/fastq_seq_count commit 7fcdca778df4012c93cb4aec26c2ff056817afee-dirty"
author | jjohnson |
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date | Tue, 26 Oct 2021 14:39:00 +0000 |
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<tool id="fastq_seq_count" name="Count sequences in fastq files" version="0.1.1" python_template_version="3.5"> <description></description> <requirements> <requirement type="package" version="3.8">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #set $qcol = int(str($query_col))-1 python $__tool_directory__/fastq_seq_count.py -p $fastqs_file -i $query_file #if $id_col #set $id_col_list = ','.join([str(int(x)-1) for x in str($id_col).split(',')]) -I '$id_col_list' #end if -q $qcol #if $query_label -Q $query_label #end if #if $compare_col #set $ccol = int(str($compare_col))-1 -c $ccol #end if #if $compare_label -C $compare_label #end if $reverse_complements -T "\${GALAXY_SLOTS:-4}" $report_fastq_counts -s $report ]]></command> <configfiles> <configfile name="fastqs_file"><![CDATA[#slurp #for $f in $fastqs: #set $line = str($f) + '\t' + $f.element_identifier $line #end for ]]></configfile> </configfiles> <inputs> <param name="fastqs" type="data" format="fastq" multiple="true" label="fastq files to search"/> <param name="query_file" type="data" format="tabular" label="query sequences"/> <param name="id_col" type="data_column" data_ref="query_file" multiple="true" optional="true" numerical="false" label="Identifier column(s)" help="Columns to keep as identifiers for the summary report"/> <param name="query_col" type="data_column" data_ref="query_file" label="query sequence column"/> <param name="query_label" type="text" value="mutant" label="query sequence label"/> <param name="compare_col" type="data_column" data_ref="query_file" optional="true" label="comparison sequence column"/> <param name="compare_label" type="text" value="normal" label="comparison sequence label"/> <param name="reverse_complements" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Also search for reverse complements"/> <param name="report_fastq_counts" type="boolean" truevalue="-n counts" falsevalue="" checked="false" label="report of per fastq counts"/> </inputs> <outputs> <data name="report" format="tabular" label="${tool.name} on ${on_string} summary report"/> <data name="hits" format="tabular" label="${tool.name} on ${on_string} count details" from_work_dir="counts"> <filter>report_fastq_counts</filter> </data> </outputs> <tests> <test> <param name="fastqs" ftype="fastq" value="reads1.fastq,reads2.fastq"/> <param name="query_file" ftype="tabular" value="query_seqs.tabular"/> <param name="id_col" value="1,2,3,4,5"/> <param name="query_col" value="4"/> <param name="query_label" value="mutant"/> <param name="compare_col" value="5"/> <param name="compare_label" value="normal"/> <param name="reverse_complements" value="True"/> <param name="report_fastq_counts" value="True"/> <output name="report" ftype="tabular" file="summary_report.out" /> <output name="hits" ftype="tabular" file="count_details.out" /> </test> </tests> <help><![CDATA[ **Report fastq reads that contain sequences** This tool searches fastq reads for given nucleic acid query sequences. A typical use would be to compare the relative occurrence of two sequences. **NOTE:** This only reports complete matches to the sequences, and reads that may partially match at the ends will not be counted. **INPUTS** fastq files - the sequence files to search query file - a tabular file - that contains a column of "query" sequences to match in fastq reads - it may contain a second "comparison" sequence column to match **OUTPUTS** summary report - a tabular file - the first column is the line number from the query file - columns from the query file selected as identifiers - the count of fastq entries for the query sequence - the count of fastq entries for the comparison sequence (if selected) - the fraction of query sequence matches compared to the total of query and comparison matches count details - an optional tabular file of match count - the fastq name - the first column is the line number from the query file - the sequence that matched - the label of the sequence that matched - the strand that matched - the number reads that matched ]]></help> </tool>