Mercurial > repos > jpayne > snp_pipeline
changeset 44:e7cac7790476
planemo upload commit 0399c6bd696435a7a99d8d8b4c237e5a78ee5856-dirty
| author | jpayne |
|---|---|
| date | Wed, 25 Apr 2018 16:35:27 -0400 |
| parents | 62531f7399dc |
| children | f58616a4b2f3 |
| files | 1_map_reads.xml test-data/samples/sample1/sample1_1.fastq.gz test-data/samples/sample1/sample1_2.fastq.gz |
| diffstat | 3 files changed, 30 insertions(+), 10 deletions(-) [+] |
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--- a/1_map_reads.xml Wed Apr 25 15:54:10 2018 -0400 +++ b/1_map_reads.xml Wed Apr 25 16:35:27 2018 -0400 @@ -9,20 +9,32 @@ <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && #if $reads.reads_select == 'collection' - export files="$reads.coll.forward $reads.coll.reverse" && - export params="-1 $reads.coll.forward -2 $reads.coll.reverse" && - #else - export files="$forward $reverse" && - export params="-1 $forward -2 $reverse" && + #set forward=$reads.coll.forward + #set reverse=$reads.coll.reverse #end if python ${__tool_directory__}/snp-cache.py snp_mapped_reads "\$(md5sum $reference - \$files + $forward + $reverse | cut -c -32 | md5sum | cut -c -32)" -c " cp $reference ./reference.fasta + #if $forward.is_of_type("fastq.gz","fastqsanger.gz") + && cp $forward ./forward.gz + #set $forward="./forward.gz" + #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2") + && cp $forward ./forward.bz2 + #set $forward="./forward.bz2" + #end if + #if $reverse.is_of_type("fastq.gz","fastqsanger.gz") + && cp $reverse ./reverse.gz + #set $reverse="./reverse.gz" + #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2") + && cp $reverse ./reverse.bz2 + #set $reverse="./reverse.bz2" + #end if && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference - && bowtie2 -q -x ./reference \$params -p \${GALAXY_SLOTS:-4} --reorder -X 1000 + && bowtie2 -q -x ./reference -1 $forward -2 $reverse -p \${GALAXY_SLOTS:-4} --reorder -X 1000 " #if $reads.reads_select == 'collection' -o ${align_from_collection} @@ -80,11 +92,11 @@ <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" collection_type="paired" /> + <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" /> - <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> + <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> @@ -121,6 +133,14 @@ </param> <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" /> </test> + <test> + <param name="source_select" value="history" /> + <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" /> + <param name="reads_select" value="history" /> + <param name="forward" value="samples/sample1/sample1_1.fastq.gz" ftype="fastqsanger.gz" /> + <param name="reverse" value="samples/sample1/sample1_2.fastq.gz" ftype="fastqsanger.gz" /> + <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" /> + </test> </tests> <help><![CDATA[ <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>