Mercurial > repos > iuc > hisat2
changeset 10:da8d655e2154 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
| author | iuc |
|---|---|
| date | Mon, 10 Apr 2017 17:40:42 -0400 |
| parents | 2dbb7f0ea66f |
| children | e926afbd9e10 |
| files | hisat2.xml hisat2_macros.xml test-data/hisat_input_2_forward.fastq.bz2 test-data/hisat_input_2_forward.fastq.gz test-data/hisat_input_2_reverse.fastq.bz2 test-data/hisat_input_2_reverse.fastq.gz |
| diffstat | 6 files changed, 127 insertions(+), 16 deletions(-) [+] |
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--- a/hisat2.xml Tue Apr 04 08:15:43 2017 -0400 +++ b/hisat2.xml Mon Apr 10 17:40:42 2017 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hisat2" name="HISAT2" version="2.0.5"> +<tool id="hisat2" name="HISAT2" version="2.0.5" profile="17.01"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> @@ -20,6 +20,9 @@ ln -s '${spliced_options.known_splice_gtf}' splice_sites.gtf && hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt && #end if + + @FASTQGZ_SETUP@ + #if $reference_genome.reference_genome_source == "history": ln -s '$reference_genome.history_item' genome.fa && hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome && @@ -28,19 +31,28 @@ #set index_path = $reference_genome.index.fields.path #end if hisat2 -p \${GALAXY_SLOTS:-1} -x '${index_path}' - #if str($input_format.paired.paired_selector) == 'paired': - -1 '${input_format.paired.reads_f}' -2 '${input_format.paired.reads_r}' - @paired_end_options@ - #else if str($input_format.paired.paired_selector) == 'paired_collection': - -1 '${input_format.paired.reads.forward}' -2 '${input_format.paired.reads.reverse}' + #if str($input_format.paired.paired_selector) != 'single': + -1 '${read1}' -2 '${read2}' @paired_end_options@ #else: - -U '${input_format.paired.reads}' + -U '${read1}' #if str( $input_format.paired.unaligned_file ) == "true": - --un '$output_unaligned_reads_l' + #if $compressed == "GZ": + --un-gz '$output_unaligned_reads_l' + #else if $compressed == "BZ2": + --un-gz '$output_unaligned_reads_l' + #else: + --un '$output_unaligned_reads_l' + #end if #end if #if str( $input_format.paired.aligned_file ) == "true": - --al '$output_aligned_reads_l' + #if $compressed == "GZ": + --al-gz '$output_aligned_reads_l' + #else if $compressed == "BZ2": + --al-bz2 '$output_aligned_reads_l' + #else: + --al '$output_aligned_reads_l' + #end if #end if #end if #if $input_format.input_format_selector == 'fasta': @@ -125,7 +137,7 @@ <expand macro="paired_input_conditional" ftype="fasta" /> </when> <when value="fastq"> - <expand macro="paired_input_conditional" ftype="fastq" /> + <expand macro="paired_input_conditional" ftype="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" /> </when> </conditional> <conditional name="reference_genome"> @@ -427,6 +439,36 @@ <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> </test> + <test><!-- Ensure fastqsanger.gz works --> + <param name="input_format_selector" value="fastq" /> + <param name="paired_selector" value="paired" /> + <param name="reference_genome_source" value="history" /> + <param name="history_item" value="phiX.fa" ftype="fasta" /> + <param name="input_options_selector" value="advanced" /> + <param name="trim_three" value="15" /> + <param name="trim_five" value="15" /> + <param name="reads_f" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" /> + <param name="reads_r" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" /> + <param name="paired_end_options_selector" value="advanced" /> + <param name="no_mixed" value="True" /> + <param name="no_discordant" value="True" /> + <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" /> + </test> + <test><!-- Ensure fastqsanger.bz2 works --> + <param name="input_format_selector" value="fastq" /> + <param name="paired_selector" value="paired" /> + <param name="reference_genome_source" value="history" /> + <param name="history_item" value="phiX.fa" ftype="fasta" /> + <param name="input_options_selector" value="advanced" /> + <param name="trim_three" value="15" /> + <param name="trim_five" value="15" /> + <param name="reads_f" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" /> + <param name="reads_r" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" /> + <param name="paired_end_options_selector" value="advanced" /> + <param name="no_mixed" value="True" /> + <param name="no_discordant" value="True" /> + <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" /> + </test> </tests> <help> <![CDATA[
--- a/hisat2_macros.xml Tue Apr 04 08:15:43 2017 -0400 +++ b/hisat2_macros.xml Mon Apr 10 17:40:42 2017 -0400 @@ -33,8 +33,8 @@ </when> <when value="single"> <param format="@FTYPE@" label="Reads" name="reads" type="data" /> - <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un" /> - <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al" /> + <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un / --un-gz" /> + <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al / --al-gz" /> </when> </conditional> </xml> @@ -55,15 +55,23 @@ </conditional> </xml> <xml name="paired_end_output"> - <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un-conc" /> - <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al-conc" /> + <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un-conc / --un-conc-gz" /> + <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al-conc / --al-conc-gz" /> </xml> <token name="@paired_end_options@"> #if str( $input_format.paired.unaligned_file ) == "true": - --un-conc '${output_unaligned_reads_l}' + #if $compressed == "GZ": + --un-conc-gz '${output_unaligned_reads_l}' + #else: + --un-conc '${output_unaligned_reads_l}' + #end if #end if #if str( $input_format.paired.aligned_file ) == "true": - --al-conc '${output_aligned_reads_l}' + #if $compressed == "GZ": + --al-conc '${output_aligned_reads_l}' + #else: + --al-conc '${output_aligned_reads_l}' + #end if #end if #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': ${input_format.paired.paired_end_options.no_mixed} @@ -77,4 +85,65 @@ #end if #end if </token> + <token name="@FASTQGZ_SETUP@"> +<![CDATA[ + #set compressed="False" + #if str($input_format.paired.paired_selector) == 'paired': + #if $input_format.paired.reads_f.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #set compressed = "GZ" + #else if $input_format.paired.reads_f.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #set compressed = "BZ2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -f -s "${input_format.paired.reads_f}" "${read1}" && + + #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read2 = "input_r.fastq.gz" + #set compressed = "GZ" + #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read2 = "input_r.fastq.bz2" + #set compressed = "BZ2" + #else: + #set read2 = "input_r.fastq" + #end if + ln -f -s "${input_format.paired.reads_r}" "${read2}" && + #else if str($input_format.paired.paired_selector) == 'paired_collection': + #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #set compressed = "GZ" + #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #set compressed = "BZ2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -s "${input_format.paired.reads.forward}" "${read1}" && + + #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read2 = "input_r.fastq.gz" + #set compressed = "GZ" + #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read2 = "input_r.fastq.bz2" + #set compressed = "BZ2" + #else: + #set read2 = "input_r.fastq" + #end if + ln -s "${input_format.paired.reads.reverse}" "${read2}" && + #else: + #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #set compressed = "GZ" + #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #set compressed = "BZ2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -s "${input_format.paired.reads}" "${read1}" && + #end if +]]> + </token> </macros>