| Previous changeset 2:2e4674c16615 (2017-03-12) Next changeset 4:95219305823a (2017-11-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a |
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modified:
bwameth.xml test-data/output.bam |
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| diff -r 2e4674c16615 -r a6ea26c1f225 bwameth.xml --- a/bwameth.xml Sun Mar 12 04:11:22 2017 -0400 +++ b/bwameth.xml Tue Apr 11 09:19:24 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="bwameth" name="bwameth" version="0.2.0.2"> +<tool id="bwameth" name="bwameth" version="0.2.0.3" profile="17.01"> <description>Fast and accurate aligner of BS-Seq reads.</description> <requirements> <requirement type="package" version="1.2">samtools</requirement> @@ -16,6 +16,55 @@ #set index=$referenceSource.index.fields.path #end if + ## Link in the files with a name that's appropriate + #if str($single_or_paired.single_or_paired_opts) == 'paired': + #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -f -s '${single_or_paired.input_mate1}' ${read1} && + + #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read2 = "input_r.fastq.gz" + #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read2 = "input_r.fastq.bz2" + #else: + #set read2 = "input_r.fastq" + #end if + ln -f -s '${single_or_paired.input_mate2}' ${read2} && + #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection': + #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -s '${single_or_paired.input_mate1.forward}' ${read1} && + + #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read2 = "input_r.fastq.gz" + #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read2 = "input_r.fastq.bz2" + #else: + #set read2 = "input_r.fastq" + #end if + ln -s '${single_or_paired.input_mate1.reverse}' ${read2} && + #else: + #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -f -s '${single_or_paired.input_singles}' ${read1} && + #end if + + bwameth.py -t "\${GALAXY_SLOTS:-4}" --reference "${index}" @@ -25,11 +74,9 @@ #end if #if $single_or_paired.single_or_paired_opts == 'single': - $single_or_paired.input_singles - #elif $single_or_paired.single_or_paired_opts == 'paired': - $single_or_paired.input_mate1 $single_or_paired.input_mate2 + $read1 #else: - $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse + $read1 $read2 #end if | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam - ]]> @@ -60,14 +107,14 @@ <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="single"> - <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." /> + <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." /> </when> <when value="paired"> - <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." /> - <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." /> + <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." /> </when> <when value="paired_collection"> - <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." /> + <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." /> </when> </conditional> <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'"> @@ -82,8 +129,8 @@ <param name="referenceSource" value="history" /> <param name="reference" value="ref.fa.gz" /> <param name="single_or_paired_opts" value="paired" /> - <param name="input_mate1" value="t_R1.fastq.gz" /> - <param name="input_mate2" value="t_R2.fastq.gz" /> + <param name="input_mate1" value="t_R1.fastq.gz"/> + <param name="input_mate2" value="t_R2.fastq.gz"/> <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> </test> <test> @@ -92,8 +139,8 @@ <param name="single_or_paired_opts" value="paired_collection" /> <param name="input_mate1"> <collection type="paired"> - <element name="forward" value="t_R1.fastq.gz" /> - <element name="reverse" value="t_R2.fastq.gz" /> + <element name="forward" value="t_R1.fastq.gz"/> + <element name="reverse" value="t_R2.fastq.gz"/> </collection> </param> <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> |
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| diff -r 2e4674c16615 -r a6ea26c1f225 test-data/output.bam |
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| Binary file test-data/output.bam has changed |