Mercurial > repos > iuc > hisat2
comparison hisat2_macros.xml @ 7:5ba8e317529a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
author | iuc |
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date | Sat, 21 Jan 2017 15:42:34 -0500 |
parents | c37b4554f794 |
children | da8d655e2154 |
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6:5f4da9ec47c7 | 7:5ba8e317529a |
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21 <conditional name="paired"> | 21 <conditional name="paired"> |
22 <expand macro="single_paired_selector" /> | 22 <expand macro="single_paired_selector" /> |
23 <when value="paired_collection"> | 23 <when value="paired_collection"> |
24 <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" /> | 24 <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" /> |
25 <expand macro="paired_end_conditional" /> | 25 <expand macro="paired_end_conditional" /> |
26 <expand macro="paired_end_output" /> | |
26 </when> | 27 </when> |
27 <when value="paired"> | 28 <when value="paired"> |
28 <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" /> | 29 <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" /> |
29 <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" /> | 30 <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" /> |
30 <expand macro="paired_end_conditional" /> | 31 <expand macro="paired_end_conditional" /> |
32 <expand macro="paired_end_output" /> | |
31 </when> | 33 </when> |
32 <when value="single"> | 34 <when value="single"> |
33 <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" /> | |
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" /> | |
34 </when> | 38 </when> |
35 </conditional> | 39 </conditional> |
36 </xml> | 40 </xml> |
37 <xml name="paired_end_conditional"> | 41 <xml name="paired_end_conditional"> |
38 <conditional name="paired_end_options"> | 42 <conditional name="paired_end_options"> |
48 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)" /> | 52 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)" /> |
49 <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." /> |
50 </when> | 54 </when> |
51 </conditional> | 55 </conditional> |
52 </xml> | 56 </xml> |
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" /> | |
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" /> | |
60 </xml> | |
53 <token name="@paired_end_options@"> | 61 <token name="@paired_end_options@"> |
62 #if str( $input_format.paired.unaligned_file ) == "true": | |
63 --un-conc '${output_unaligned_reads_l}' | |
64 #end if | |
65 #if str( $input_format.paired.aligned_file ) == "true": | |
66 --al-conc '${output_aligned_reads_l}' | |
67 #end if | |
54 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': | 68 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': |
55 ${input_format.paired.paired_end_options.no_mixed} | 69 ${input_format.paired.paired_end_options.no_mixed} |
56 ${input_format.paired.paired_end_options.no_discordant} | 70 ${input_format.paired.paired_end_options.no_discordant} |
57 #end if | 71 #end if |
58 </token> | 72 </token> |