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comparison hisat2_macros.xml @ 14:526b91fbde60 draft

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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
comparison
equal deleted inserted replaced
13:f4fa77189eb0 14:526b91fbde60
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="single_paired_selector"> 3 <xml name="single_paired_selector">
4 <param label="Single end or paired reads?" name="paired_selector" type="select"> 4 <param name="paired_selector" type="select" label="Single end or paired reads?">
5 <option value="paired_collection">Collection of paired reads</option> 5 <option value="paired">Paired reads</option>
6 <option value="paired">Individual paired reads</option> 6 <option value="single">Unpaired reads</option>
7 <option value="single">Individual unpaired reads</option>
8 </param> 7 </param>
9 </xml> 8 </xml>
10 <xml name="paired_input_conditional" tokens="ftype"> 9 <xml name="paired_input_conditional" tokens="ftype">
11 <conditional name="paired"> 10 <conditional name="paired">
12 <expand macro="single_paired_selector" /> 11 <expand macro="single_paired_selector" />
13 <when value="paired_collection">
14 <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
15 <expand macro="paired_end_conditional" />
16 <expand macro="paired_end_output" />
17 </when>
18 <when value="paired"> 12 <when value="paired">
19 <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" /> 13 <conditional name="collection" label="Data structure">
20 <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" /> 14 <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">
15 <option value="files">Individual files</option>
16 <option value="collection">Pair collection or list of pairs</option>
17 </param>
18 <when value="collection">
19 <param name="reads" type="data_collection" collection_type="paired" format="@FTYPE@" label="Paired reads" />
20 </when>
21 <when value="files">
22 <param name="forward" type="data" format="@FTYPE@" label="Forward reads" />
23 <param name="reverse" type="data" format="@FTYPE@" label="Reverse reads" />
24 </when>
25 </conditional>
21 <expand macro="paired_end_conditional" /> 26 <expand macro="paired_end_conditional" />
22 <expand macro="paired_end_output" /> 27 <expand macro="paired_end_output" />
23 </when> 28 </when>
24 <when value="single"> 29 <when value="single">
25 <param format="@FTYPE@" label="Reads" name="reads" type="data" /> 30 <param name="reads" type="data" format="@FTYPE@" label="Reads" />
26 <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" /> 31 <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)" />
27 <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" /> 32 <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)" />
28 </when> 33 </when>
29 </conditional> 34 </conditional>
30 </xml> 35 </xml>
31 <xml name="paired_end_conditional"> 36 <xml name="paired_end_conditional">
32 <conditional name="paired_end_options"> 37 <conditional name="paired_end_options">
33 <param label="Paired-end options" name="paired_end_options_selector" type="select"> 38 <param name="paired_end_options_selector" type="select" label="Paired-end options">
34 <option value="defaults">Use default values</option> 39 <option value="defaults">Use default values</option>
35 <option value="advanced">Specify paired-end parameters</option> 40 <option value="advanced">Specify paired-end parameters</option>
36 </param> 41 </param>
37 <when value="defaults" /> 42 <when value="defaults" />
38 <when value="advanced"> 43 <when value="advanced">
39 <param name="no_mixed" label="Disable alignments of individual mates" type="boolean" truevalue="--no-mixed" falsevalue="" 44 <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" />
40 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)" /> 45 <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" />
41 <param name="no_discordant" label="Disable discordant alignments" type="boolean" truevalue="--no-discordant" falsevalue="" 46 <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" />
42 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)" />
43 <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." />
44 </when> 47 </when>
45 </conditional> 48 </conditional>
46 </xml> 49 </xml>
47 <xml name="paired_end_output"> 50 <xml name="paired_end_output">
48 <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" /> 51 <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)" />
49 <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" /> 52 <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)" />
50 </xml> 53 </xml>
51 <token name="@paired_end_options@"> 54 <token name="@paired_end_options@">
52 #if str( $input_format.paired.unaligned_file ) == "true": 55 #if str( $input_format.paired.unaligned_file ) == "true":
53 #if $compressed == "GZ": 56 #if $compressed == "GZ":
54 --un-conc-gz '${output_unaligned_reads_l}' 57 --un-conc-gz '${output_unaligned_reads_l}'
64 #else if $compressed == "BZ2" 67 #else if $compressed == "BZ2"
65 --al-conc-bz2 '${output_aligned_reads_l}' 68 --al-conc-bz2 '${output_aligned_reads_l}'
66 #else: 69 #else:
67 --al-conc '${output_aligned_reads_l}' 70 --al-conc '${output_aligned_reads_l}'
68 #end if 71 #end if
69 #end if 72 #end if
70 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': 73 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
71 ${input_format.paired.paired_end_options.no_mixed} 74 ${input_format.paired.paired_end_options.no_mixed}
72 ${input_format.paired.paired_end_options.no_discordant} 75 ${input_format.paired.paired_end_options.no_discordant}
73 #end if 76 #end if
74 </token> 77 </token>
81 </token> 84 </token>
82 <token name="@FASTQGZ_SETUP@"> 85 <token name="@FASTQGZ_SETUP@">
83 <![CDATA[ 86 <![CDATA[
84 #set compressed="False" 87 #set compressed="False"
85 #if str($input_format.paired.paired_selector) == 'paired': 88 #if str($input_format.paired.paired_selector) == 'paired':
86 #if $input_format.paired.reads_f.is_of_type("fastq.gz", "fastqsanger.gz"): 89 #if str($input_format.paired.collection.collection_selector) == 'collection':
87 #set read1 = "input_f.fastq.gz" 90 #if $input_format.paired.collection.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
88 #set compressed = "GZ" 91 #set read1 = "input_f.fastq.gz"
89 #else if $input_format.paired.reads_f.is_of_type("fastq.bz2", "fastqsanger.bz2"): 92 #set compressed = "GZ"
90 #set read1 = "input_f.fastq.bz2" 93 #else if $input_format.paired.collection.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
91 #set compressed = "BZ2" 94 #set read1 = "input_f.fastq.bz2"
95 #set compressed = "BZ2"
96 #else:
97 #set read1 = "input_f.fastq"
98 #end if
99 ln -f -s '${input_format.paired.collection.reads.forward}' ${read1} &&
100
101 #if $input_format.paired.collection.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
102 #set read2 = "input_r.fastq.gz"
103 #set compressed = "GZ"
104 #else if $input_format.paired.collection.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
105 #set read2 = "input_r.fastq.bz2"
106 #set compressed = "BZ2"
107 #else:
108 #set read2 = "input_r.fastq"
109 #end if
110 ln -f -s '${input_format.paired.collection.reads.reverse}' ${read2} &&
92 #else: 111 #else:
93 #set read1 = "input_f.fastq" 112 #if $input_format.paired.collection.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
113 #set read1 = "input_f.fastq.gz"
114 #set compressed = "GZ"
115 #else if $input_format.paired.collection.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
116 #set read1 = "input_f.fastq.bz2"
117 #set compressed = "BZ2"
118 #else:
119 #set read1 = "input_f.fastq"
120 #end if
121 ln -f -s '${input_format.paired.collection.forward}' ${read1} &&
122
123 #if $input_format.paired.collection.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
124 #set read2 = "input_r.fastq.gz"
125 #set compressed = "GZ"
126 #else if $input_format.paired.collection.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
127 #set read2 = "input_r.fastq.bz2"
128 #set compressed = "BZ2"
129 #else:
130 #set read2 = "input_r.fastq"
131 #end if
132 ln -f -s '${input_format.paired.collection.reverse}' ${read2} &&
94 #end if 133 #end if
95 ln -f -s '${input_format.paired.reads_f}' ${read1} &&
96
97 #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"):
98 #set read2 = "input_r.fastq.gz"
99 #set compressed = "GZ"
100 #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"):
101 #set read2 = "input_r.fastq.bz2"
102 #set compressed = "BZ2"
103 #else:
104 #set read2 = "input_r.fastq"
105 #end if
106 ln -f -s '${input_format.paired.reads_r}' ${read2} &&
107 #else if str($input_format.paired.paired_selector) == 'paired_collection':
108 #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
109 #set read1 = "input_f.fastq.gz"
110 #set compressed = "GZ"
111 #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
112 #set read1 = "input_f.fastq.bz2"
113 #set compressed = "BZ2"
114 #else:
115 #set read1 = "input_f.fastq"
116 #end if
117 ln -s '${input_format.paired.reads.forward}' ${read1} &&
118
119 #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
120 #set read2 = "input_r.fastq.gz"
121 #set compressed = "GZ"
122 #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
123 #set read2 = "input_r.fastq.bz2"
124 #set compressed = "BZ2"
125 #else:
126 #set read2 = "input_r.fastq"
127 #end if
128 ln -s '${input_format.paired.reads.reverse}' ${read2} &&
129 #else: 134 #else:
130 #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"): 135 #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):
131 #set read1 = "input_f.fastq.gz" 136 #set read1 = "input_f.fastq.gz"
132 #set compressed = "GZ" 137 #set compressed = "GZ"
133 #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"): 138 #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"):