Mercurial > repos > devteam > bowtie2
diff bowtie2_wrapper.xml @ 16:8ccbdbe9a695 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
| author | iuc |
|---|---|
| date | Thu, 01 Jun 2017 11:14:22 -0400 |
| parents | 43d12513224b |
| children | 66f992977578 |
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--- a/bowtie2_wrapper.xml Thu Jun 01 06:47:03 2017 -0400 +++ b/bowtie2_wrapper.xml Thu Jun 01 11:14:22 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="bowtie2" name="Bowtie2" version="2.3.2.1" profile="17.01"> +<tool id="bowtie2" name="Bowtie2" version="2.3.2.2" profile="17.01"> <description>- map reads against reference genome</description> <macros> <import>bowtie2_macros.xml</import> @@ -22,6 +22,7 @@ ## Link in the input files, so bowtie2 can tell their type #set compressed="False" + #set reads_are_fastq = True #if str($library.type) == 'paired': #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" @@ -29,6 +30,9 @@ #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read1 = "input_f.fastq.bz2" #set compressed = "BZ2" + #else if $library.input_1.is_of_type('fasta'): + #set reads_are_fastq = False + #set read1 = "input_f.fasta" #else: #set read1 = "input_f.fastq" #end if @@ -40,6 +44,8 @@ #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read2 = "input_r.fastq.bz2" #set compressed = "BZ2" + #else if $library.input_2.is_of_type('fasta'): + #set read2 = "input_r.fasta" #else: #set read2 = "input_r.fastq" #end if @@ -51,6 +57,9 @@ #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read1 = "input_f.fastq.bz2" #set compressed = "BZ2" + #else if $library.input_1.forward.is_of_type('fasta'): + #set reads_are_fastq = False + #set read1 = "input_f.fasta" #else: #set read1 = "input_f.fastq" #end if @@ -62,6 +71,8 @@ #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read2 = "input_r.fastq.bz2" #set compressed = "BZ2" + #else if $library.input_1.reverse.is_of_type("fasta"): + #set read2 = "input_r.fasta" #else: #set read2 = "input_r.fastq" #end if @@ -74,6 +85,9 @@ #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read1 = "input_il.fastq.bz2" #set compressed = "BZ2" + #else if $library.input_1.is_of_type("fasta"): + #set reads_are_fastq = False + #set read1 = "input_il.fasta" #else: #set read1 = "input_il.fastq" #end if @@ -85,6 +99,9 @@ #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read1 = "input_f.fastq.bz2" #set compressed = "BZ2" + #else if $library.input_1.is_of_type("fasta"): + #set reads_are_fastq = False + #set read1 = "input_f.fasta" #else: #set read1 = "input_f.fastq" #end if @@ -101,7 +118,12 @@ ## index file path -x '$index_path' - ## Fastq inputs + ## Input reads are fasta? + #if not reads_are_fastq: + -f + #end if + + ## Input reads #if str( $library.type ) == "single": -U '${read1}' #if str( $library.unaligned_file ) == "true": @@ -310,28 +332,28 @@ </param> <when value="single"> - <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> + <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype "fastqsanger" or "fasta"" /> <expand macro="align_unalign" /> </when> <when value="paired"> - <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> - <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> + <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype "fastqsanger"or "fasta"" /> + <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype "fastqsanger"or "fasta"" /> <expand macro="align_unalign" /> <expand macro="paired_end_options" /> </when> <when value="paired_collection"> - <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger"" /> + <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" /> <expand macro="align_unalign" /> <expand macro="paired_end_options" /> </when> <when value="paired_interleaved"> - <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger". --interleaved"/> + <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/> <expand macro="align_unalign" /> <expand macro="paired_end_options" /> @@ -728,6 +750,18 @@ <param name="own_file" value="bowtie2-ref.fasta" /> <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> </test> + <test> + <!-- test fasta input --> + <param name="type" value="paired"/> + <param name="paired_options_selector" value="no"/> + <param name="unaligned_file" value="false"/> + <param name="analysis_type_selector" value="simple"/> + <param name="source" value="history" /> + <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> + <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> + <param name="own_file" value="bowtie2-ref.fasta" /> + <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> + </test> </tests> <help><![CDATA[