Mercurial > repos > jpayne > confindr
changeset 0:619d56f369af
"planemo upload commit e779d2916df6a1f2f5884c3abfac3bf3a1e59717"
| author | jpayne |
|---|---|
| date | Thu, 03 Sep 2020 22:32:44 -0400 |
| parents | |
| children | fa7e2cc36ceb |
| files | confindr.xml test-data/confindr_report.csv test-data/confindr_report_2.csv test-data/example_R1.fastq.bz2 test-data/example_R1.fastq.gz test-data/example_R2.fastq.bz2 test-data/example_R2.fastq.gz |
| diffstat | 7 files changed, 95 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confindr.xml Thu Sep 03 22:32:44 2020 -0400 @@ -0,0 +1,91 @@ +<tool id="confindr" name="ConFindr" version="0.1.0" python_template_version="3.5"> + <requirements> + <requirement type="package" version="0.7.4">confindr</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $reads.reads_select == 'collection' + #set forward=$reads.coll.forward + #set reverse=$reads.coll.reverse + #set name=$reads.coll.name.replace(' ', '_') + #else + #set name=$forward.name.split('_')[0] + #end if + mkdir ./${name} + #if $forward.is_of_type("fastq.gz","fastqsanger.gz") + && cp $forward ./${name}/${name}_R1.fastq.gz + #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2") + && tar -vxjOf $forward > ./${name}/${name}_R1.fastq + #else + && cp $forward ./${name}/${name}_R1.fastq + #end if + #if $reverse.is_of_type("fastq.gz","fastqsanger.gz") + && cp $reverse ./${name}/${name}_R2.fastq.gz + #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2") + && tar -vxjOf $reverse > ./${name}/${name}_R2.fastq + #else + && cp $reverse ./${name}/${name}_R2.fastq + #end if + ## !!! confindr in single-threaded mode; race condition bugs in multiple threads !!! ## + && confindr.py -i ./${name} -o ./output -t 1 + && cat ./output/confindr_log.txt + && ls -lah ./output/confindr_report.csv + + ]]></command> + <inputs> + <conditional name="reads"> + <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> + <option value="collection">Paired collection from your history</option> + <option value="history">Two FASTQ datasets from your history</option> + </param> + <when value="collection"> + <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> + </when> + <when value="history"> + <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" /> + <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="csv" name="contam_report" label="Contamination Report" from_work_dir="./output/confindr_report.csv" /> + </outputs> + <tests> + <test> + <param name="reads_select" value="collection" /> + <param name="coll"> + <collection type="paired"> + <element name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz" /> + </collection> + </param> + <output name="contam_report" value="confindr_report.csv" /> + </test> + <test> + <param name="reads_select" value="history" /> + <param name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz"/> + <param name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz"/> + <output name="contam_report" value="confindr_report_2.csv" /> + </test> + <test> + <param name="reads_select" value="history" /> + <param name="forward" value="example_R1.fastq.bz2" ftype="fastqsanger.bz2"/> + <param name="reverse" value="example_R2.fastq.bz2" ftype="fastqsanger.bz2"/> + <output name="contam_report" value="confindr_report_2.csv" /> + </test> + </tests> + <help><![CDATA[ + ConFindr, a contamination screen for Illumina sequencing + ]]></help> + <citations> + <citation type="doi">10.7717/peerj.6995</citation> + <citation type="bibtex"> +@misc{githubConFindr, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {ConFindr}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/OLC-Bioinformatics/ConFindr}, +}</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/confindr_report.csv Thu Sep 03 22:32:44 2020 -0400 @@ -0,0 +1,2 @@ +Sample,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamStandardDeviation,BasesExamined,DatabaseDownloadDate +Unnamed_Collection,Error processing sample,0,False,ND,ND,0,ND
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/confindr_report_2.csv Thu Sep 03 22:32:44 2020 -0400 @@ -0,0 +1,2 @@ +Sample,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamStandardDeviation,BasesExamined,DatabaseDownloadDate +example,Error processing sample,0,False,ND,ND,0,ND