Mercurial > repos > iuc > hisat2
comparison hisat2_macros.xml @ 0:5bafe7d7a55e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
author | iuc |
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date | Sat, 10 Oct 2015 14:54:39 -0400 |
parents | |
children | c37b4554f794 |
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-1:000000000000 | 0:5bafe7d7a55e |
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1 <?xml version="1.0"?> | |
2 <macros> | |
3 <xml name="function" tokens="helptext"> | |
4 <param display="radio" help="@HELPTEXT@" label="Function type" name="function_type" type="select"> | |
5 <option value="C">Constant</option> | |
6 <option value="L">Linear [f(x) = y + z * x]</option> | |
7 <option value="S">Square root [f(x) = y + z * x²]</option> | |
8 <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option> | |
9 </param> | |
10 <param help="@HELPTEXT@" label="Constant term (y)" name="constant_term" type="integer" value="0" /> | |
11 <param help="@HELPTEXT@" label="Coefficient (z)" name="coefficient" type="integer" value="0" /> | |
12 </xml> | |
13 <xml name="single_paired_selector"> | |
14 <param label="Single end or paired reads?" name="paired_selector" type="select"> | |
15 <option value="paired_collection">Collection of paired reads</option> | |
16 <option value="paired">Individual paired reads</option> | |
17 <option value="single">Individual unpaired reads</option> | |
18 </param> | |
19 </xml> | |
20 <xml name="paired_input_conditional" tokens="ftype"> | |
21 <conditional name="paired"> | |
22 <expand macro="single_paired_selector" /> | |
23 <when value="paired_collection"> | |
24 <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" /> | |
25 <expand macro="paired_end_conditional" /> | |
26 </when> | |
27 <when value="paired"> | |
28 <param format="@FTYPE@" label="Forward reads" multiple="true" name="reads_f" type="data" /> | |
29 <param format="@FTYPE@" label="Reverse reads" multiple="true" name="reads_r" type="data" /> | |
30 <expand macro="paired_end_conditional" /> | |
31 </when> | |
32 <when value="single"> | |
33 <param format="@FTYPE@" label="Reads" multiple="true" name="reads" type="data" /> | |
34 </when> | |
35 </conditional> | |
36 </xml> | |
37 <xml name="paired_end_conditional"> | |
38 <conditional name="paired_end_options"> | |
39 <param label="Paired-end options" name="paired_end_options_selector" type="select"> | |
40 <option value="defaults">Use default values</option> | |
41 <option value="advanced">Specify paired-end parameters</option> | |
42 </param> | |
43 <when value="defaults" /> | |
44 <when value="advanced"> | |
45 <param name="no_mixed" label="Disable alignments of individual mates" type="boolean" truevalue="--no-mixed" falsevalue="" | |
46 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)" /> | |
47 <param name="no_discordant" label="Disable discordant alignments" type="boolean" truevalue="--no-discordant" falsevalue="" | |
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)" /> | |
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." /> | |
50 </when> | |
51 </conditional> | |
52 </xml> | |
53 <token name="@paired_end_options@"> | |
54 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': | |
55 ${input_format.paired.paired_end_options.no_mixed} | |
56 ${input_format.paired.paired_end_options.no_discordant} | |
57 #end if | |
58 </token> | |
59 <token name="strandedness_parameters"> | |
60 #if str($spliced_options.spliced_options_selector) == "advanced": | |
61 #if str($spliced_options.rna_strandness).strip() != '': | |
62 --rna-strandness $spliced_options.rna_strandness | |
63 #end if | |
64 #end if | |
65 </token> | |
66 </macros> |