Mercurial > repos > iuc > hisat2
diff hisat2_macros.xml @ 14:526b91fbde60 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
author | iuc |
---|---|
date | Wed, 19 Jul 2017 04:57:27 -0400 |
parents | f4fa77189eb0 |
children | d5fe9aead222 |
line wrap: on
line diff
--- a/hisat2_macros.xml Tue Jul 18 14:25:13 2017 -0400 +++ b/hisat2_macros.xml Wed Jul 19 04:57:27 2017 -0400 @@ -1,52 +1,55 @@ <?xml version="1.0"?> <macros> <xml name="single_paired_selector"> - <param label="Single end or paired reads?" name="paired_selector" type="select"> - <option value="paired_collection">Collection of paired reads</option> - <option value="paired">Individual paired reads</option> - <option value="single">Individual unpaired reads</option> + <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_collection"> - <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" /> - <expand macro="paired_end_conditional" /> - <expand macro="paired_end_output" /> - </when> <when value="paired"> - <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" /> - <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" /> + <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 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 / --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" /> + <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 label="Paired-end options" name="paired_end_options_selector" type="select"> + <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" label="Disable alignments of individual mates" type="boolean" truevalue="--no-mixed" falsevalue="" - 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. (--no-mixed)" /> - <param name="no_discordant" label="Disable discordant alignments" type="boolean" truevalue="--no-discordant" falsevalue="" - 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. (--no-discordant)" /> - <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) 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." /> + <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" 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" /> + <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( $input_format.paired.unaligned_file ) == "true": @@ -66,7 +69,7 @@ #else: --al-conc '${output_aligned_reads_l}' #end if - #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} ${input_format.paired.paired_end_options.no_discordant} @@ -83,49 +86,51 @@ <![CDATA[ #set compressed="False" #if str($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 $input_format.paired.reads_f.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = "input_f.fastq.bz2" - #set compressed = "BZ2" + #if str($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}' ${read2} && #else: - #set read1 = "input_f.fastq" - #end if - ln -f -s '${input_format.paired.reads_f}' ${read1} && + #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.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" + #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}' ${read2} && #end if - ln -f -s '${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"