Mercurial > repos > iuc > hisat2
view hisat2_macros.xml @ 14:526b91fbde60 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
author | iuc |
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date | Wed, 19 Jul 2017 04:57:27 -0400 |
parents | f4fa77189eb0 |
children | d5fe9aead222 |
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<?xml version="1.0"?> <macros> <xml name="single_paired_selector"> <param name="paired_selector" type="select" label="Single end or paired reads?"> <option value="paired">Paired reads</option> <option value="single">Unpaired reads</option> </param> </xml> <xml name="paired_input_conditional" tokens="ftype"> <conditional name="paired"> <expand macro="single_paired_selector" /> <when value="paired"> <conditional name="collection" label="Data structure"> <param name="collection_selector" type="select" label="Input is structured as" help="If a list of pairs is selected, HISAT2 will run in batch mode over each pair in the list, producing a list of output bam files"> <option value="files">Individual files</option> <option value="collection">Pair collection or list of pairs</option> </param> <when value="collection"> <param name="reads" type="data_collection" collection_type="paired" format="@FTYPE@" label="Paired reads" /> </when> <when value="files"> <param name="forward" type="data" format="@FTYPE@" label="Forward reads" /> <param name="reverse" type="data" format="@FTYPE@" label="Reverse reads" /> </when> </conditional> <expand macro="paired_end_conditional" /> <expand macro="paired_end_output" /> </when> <when value="single"> <param name="reads" type="data" format="@FTYPE@" label="Reads" /> <param name="unaligned_file" argument="--un-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" /> <param name="aligned_file" argument="--al-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" /> </when> </conditional> </xml> <xml name="paired_end_conditional"> <conditional name="paired_end_options"> <param name="paired_end_options_selector" type="select" label="Paired-end options"> <option value="defaults">Use default values</option> <option value="advanced">Specify paired-end parameters</option> </param> <when value="defaults" /> <when value="advanced"> <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" label="Disable alignments of individual mates" help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior" /> <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" label="Disable alignments of individual mates" help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior" /> <param name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reference strand of reference" help="If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" /> </when> </conditional> </xml> <xml name="paired_end_output"> <param name="unaligned_file" argument="--un-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" /> <param name="aligned_file" argument="--al-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" /> </xml> <token name="@paired_end_options@"> #if str( $input_format.paired.unaligned_file ) == "true": #if $compressed == "GZ": --un-conc-gz '${output_unaligned_reads_l}' #else if $compressed == "BZ2": --un-conc-bz2 '${output_unaligned_reads_l}' #else: --un-conc '${output_unaligned_reads_l}' #end if #end if #if str( $input_format.paired.aligned_file ) == "true": #if $compressed == "GZ": --al-conc-gz '${output_aligned_reads_l}' #else if $compressed == "BZ2" --al-conc-bz2 '${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} ${input_format.paired.paired_end_options.no_discordant} #end if </token> <token name="@strandedness_parameters@"> #if str($spliced_options.spliced_options_selector) == "advanced": #if str($spliced_options.rna_strandness).strip() != '': --rna-strandness $spliced_options.rna_strandness #end if #end if </token> <token name="@FASTQGZ_SETUP@"> <![CDATA[ #set compressed="False" #if str($input_format.paired.paired_selector) == 'paired': #if str($input_format.paired.collection.collection_selector) == 'collection': #if $input_format.paired.collection.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" #set compressed = "GZ" #else if $input_format.paired.collection.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read1 = "input_f.fastq.bz2" #set compressed = "BZ2" #else: #set read1 = "input_f.fastq" #end if ln -f -s '${input_format.paired.collection.reads.forward}' ${read1} && #if $input_format.paired.collection.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): #set read2 = "input_r.fastq.gz" #set compressed = "GZ" #else if $input_format.paired.collection.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read2 = "input_r.fastq.bz2" #set compressed = "BZ2" #else: #set read2 = "input_r.fastq" #end if ln -f -s '${input_format.paired.collection.reads.reverse}' ${read2} && #else: #if $input_format.paired.collection.forward.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" #set compressed = "GZ" #else if $input_format.paired.collection.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read1 = "input_f.fastq.bz2" #set compressed = "BZ2" #else: #set read1 = "input_f.fastq" #end if ln -f -s '${input_format.paired.collection.forward}' ${read1} && #if $input_format.paired.collection.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): #set read2 = "input_r.fastq.gz" #set compressed = "GZ" #else if $input_format.paired.collection.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set read2 = "input_r.fastq.bz2" #set compressed = "BZ2" #else: #set read2 = "input_r.fastq" #end if ln -f -s '${input_format.paired.collection.reverse}' ${read2} && #end if #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>