Mercurial > repos > iuc > hisat2
comparison hisat2_macros.xml @ 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 | 5ba8e317529a |
| children | e926afbd9e10 |
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| 9:2dbb7f0ea66f | 10:da8d655e2154 |
|---|---|
| 31 <expand macro="paired_end_conditional" /> | 31 <expand macro="paired_end_conditional" /> |
| 32 <expand macro="paired_end_output" /> | 32 <expand macro="paired_end_output" /> |
| 33 </when> | 33 </when> |
| 34 <when value="single"> | 34 <when value="single"> |
| 35 <param format="@FTYPE@" label="Reads" name="reads" type="data" /> | 35 <param format="@FTYPE@" label="Reads" name="reads" type="data" /> |
| 36 <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" /> | 36 <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" /> |
| 37 <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" /> | 37 <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" /> |
| 38 </when> | 38 </when> |
| 39 </conditional> | 39 </conditional> |
| 40 </xml> | 40 </xml> |
| 41 <xml name="paired_end_conditional"> | 41 <xml name="paired_end_conditional"> |
| 42 <conditional name="paired_end_options"> | 42 <conditional name="paired_end_options"> |
| 53 <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." /> | 53 <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." /> |
| 54 </when> | 54 </when> |
| 55 </conditional> | 55 </conditional> |
| 56 </xml> | 56 </xml> |
| 57 <xml name="paired_end_output"> | 57 <xml name="paired_end_output"> |
| 58 <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" /> | 58 <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" /> |
| 59 <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" /> | 59 <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" /> |
| 60 </xml> | 60 </xml> |
| 61 <token name="@paired_end_options@"> | 61 <token name="@paired_end_options@"> |
| 62 #if str( $input_format.paired.unaligned_file ) == "true": | 62 #if str( $input_format.paired.unaligned_file ) == "true": |
| 63 --un-conc '${output_unaligned_reads_l}' | 63 #if $compressed == "GZ": |
| 64 --un-conc-gz '${output_unaligned_reads_l}' | |
| 65 #else: | |
| 66 --un-conc '${output_unaligned_reads_l}' | |
| 67 #end if | |
| 64 #end if | 68 #end if |
| 65 #if str( $input_format.paired.aligned_file ) == "true": | 69 #if str( $input_format.paired.aligned_file ) == "true": |
| 66 --al-conc '${output_aligned_reads_l}' | 70 #if $compressed == "GZ": |
| 71 --al-conc '${output_aligned_reads_l}' | |
| 72 #else: | |
| 73 --al-conc '${output_aligned_reads_l}' | |
| 74 #end if | |
| 67 #end if | 75 #end if |
| 68 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': | 76 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': |
| 69 ${input_format.paired.paired_end_options.no_mixed} | 77 ${input_format.paired.paired_end_options.no_mixed} |
| 70 ${input_format.paired.paired_end_options.no_discordant} | 78 ${input_format.paired.paired_end_options.no_discordant} |
| 71 #end if | 79 #end if |
| 75 #if str($spliced_options.rna_strandness).strip() != '': | 83 #if str($spliced_options.rna_strandness).strip() != '': |
| 76 --rna-strandness $spliced_options.rna_strandness | 84 --rna-strandness $spliced_options.rna_strandness |
| 77 #end if | 85 #end if |
| 78 #end if | 86 #end if |
| 79 </token> | 87 </token> |
| 88 <token name="@FASTQGZ_SETUP@"> | |
| 89 <![CDATA[ | |
| 90 #set compressed="False" | |
| 91 #if str($input_format.paired.paired_selector) == 'paired': | |
| 92 #if $input_format.paired.reads_f.is_of_type("fastq.gz", "fastqsanger.gz"): | |
| 93 #set read1 = "input_f.fastq.gz" | |
| 94 #set compressed = "GZ" | |
| 95 #else if $input_format.paired.reads_f.is_of_type("fastq.bz2", "fastqsanger.bz2"): | |
| 96 #set read1 = "input_f.fastq.bz2" | |
| 97 #set compressed = "BZ2" | |
| 98 #else: | |
| 99 #set read1 = "input_f.fastq" | |
| 100 #end if | |
| 101 ln -f -s "${input_format.paired.reads_f}" "${read1}" && | |
| 102 | |
| 103 #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"): | |
| 104 #set read2 = "input_r.fastq.gz" | |
| 105 #set compressed = "GZ" | |
| 106 #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"): | |
| 107 #set read2 = "input_r.fastq.bz2" | |
| 108 #set compressed = "BZ2" | |
| 109 #else: | |
| 110 #set read2 = "input_r.fastq" | |
| 111 #end if | |
| 112 ln -f -s "${input_format.paired.reads_r}" "${read2}" && | |
| 113 #else if str($input_format.paired.paired_selector) == 'paired_collection': | |
| 114 #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"): | |
| 115 #set read1 = "input_f.fastq.gz" | |
| 116 #set compressed = "GZ" | |
| 117 #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): | |
| 118 #set read1 = "input_f.fastq.bz2" | |
| 119 #set compressed = "BZ2" | |
| 120 #else: | |
| 121 #set read1 = "input_f.fastq" | |
| 122 #end if | |
| 123 ln -s "${input_format.paired.reads.forward}" "${read1}" && | |
| 124 | |
| 125 #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): | |
| 126 #set read2 = "input_r.fastq.gz" | |
| 127 #set compressed = "GZ" | |
| 128 #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): | |
| 129 #set read2 = "input_r.fastq.bz2" | |
| 130 #set compressed = "BZ2" | |
| 131 #else: | |
| 132 #set read2 = "input_r.fastq" | |
| 133 #end if | |
| 134 ln -s "${input_format.paired.reads.reverse}" "${read2}" && | |
| 135 #else: | |
| 136 #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"): | |
| 137 #set read1 = "input_f.fastq.gz" | |
| 138 #set compressed = "GZ" | |
| 139 #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"): | |
| 140 #set read1 = "input_f.fastq.bz2" | |
| 141 #set compressed = "BZ2" | |
| 142 #else: | |
| 143 #set read1 = "input_f.fastq" | |
| 144 #end if | |
| 145 ln -s "${input_format.paired.reads}" "${read1}" && | |
| 146 #end if | |
| 147 ]]> | |
| 148 </token> | |
| 80 </macros> | 149 </macros> |