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comparison hisat2_macros.xml @ 11:e926afbd9e10 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty
author iuc
date Mon, 10 Apr 2017 23:17:56 -0400
parents da8d655e2154
children f4fa77189eb0
comparison
equal deleted inserted replaced
10:da8d655e2154 11:e926afbd9e10
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 #if $compressed == "GZ": 63 #if $compressed == "GZ":
64 --un-conc-gz '${output_unaligned_reads_l}' 64 --un-conc-gz '${output_unaligned_reads_l}'
65 #else if $compressed == "BZ2":
66 --un-conc-bz2 '${output_unaligned_reads_l}'
65 #else: 67 #else:
66 --un-conc '${output_unaligned_reads_l}' 68 --un-conc '${output_unaligned_reads_l}'
67 #end if 69 #end if
68 #end if 70 #end if
69 #if str( $input_format.paired.aligned_file ) == "true": 71 #if str( $input_format.paired.aligned_file ) == "true":
70 #if $compressed == "GZ": 72 #if $compressed == "GZ":
71 --al-conc '${output_aligned_reads_l}' 73 --al-conc-gz '${output_aligned_reads_l}'
74 #else if $compressed == "BZ2"
75 --al-conc-bz2 '${output_aligned_reads_l}'
72 #else: 76 #else:
73 --al-conc '${output_aligned_reads_l}' 77 --al-conc '${output_aligned_reads_l}'
74 #end if 78 #end if
75 #end if 79 #end if
76 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': 80 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
96 #set read1 = "input_f.fastq.bz2" 100 #set read1 = "input_f.fastq.bz2"
97 #set compressed = "BZ2" 101 #set compressed = "BZ2"
98 #else: 102 #else:
99 #set read1 = "input_f.fastq" 103 #set read1 = "input_f.fastq"
100 #end if 104 #end if
101 ln -f -s "${input_format.paired.reads_f}" "${read1}" && 105 ln -f -s '${input_format.paired.reads_f}' ${read1} &&
102 106
103 #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"): 107 #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"):
104 #set read2 = "input_r.fastq.gz" 108 #set read2 = "input_r.fastq.gz"
105 #set compressed = "GZ" 109 #set compressed = "GZ"
106 #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"): 110 #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"):
107 #set read2 = "input_r.fastq.bz2" 111 #set read2 = "input_r.fastq.bz2"
108 #set compressed = "BZ2" 112 #set compressed = "BZ2"
109 #else: 113 #else:
110 #set read2 = "input_r.fastq" 114 #set read2 = "input_r.fastq"
111 #end if 115 #end if
112 ln -f -s "${input_format.paired.reads_r}" "${read2}" && 116 ln -f -s '${input_format.paired.reads_r}' ${read2} &&
113 #else if str($input_format.paired.paired_selector) == 'paired_collection': 117 #else if str($input_format.paired.paired_selector) == 'paired_collection':
114 #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"): 118 #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
115 #set read1 = "input_f.fastq.gz" 119 #set read1 = "input_f.fastq.gz"
116 #set compressed = "GZ" 120 #set compressed = "GZ"
117 #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): 121 #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
118 #set read1 = "input_f.fastq.bz2" 122 #set read1 = "input_f.fastq.bz2"
119 #set compressed = "BZ2" 123 #set compressed = "BZ2"
120 #else: 124 #else:
121 #set read1 = "input_f.fastq" 125 #set read1 = "input_f.fastq"
122 #end if 126 #end if
123 ln -s "${input_format.paired.reads.forward}" "${read1}" && 127 ln -s '${input_format.paired.reads.forward}' ${read1} &&
124 128
125 #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): 129 #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
126 #set read2 = "input_r.fastq.gz" 130 #set read2 = "input_r.fastq.gz"
127 #set compressed = "GZ" 131 #set compressed = "GZ"
128 #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): 132 #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
129 #set read2 = "input_r.fastq.bz2" 133 #set read2 = "input_r.fastq.bz2"
130 #set compressed = "BZ2" 134 #set compressed = "BZ2"
131 #else: 135 #else:
132 #set read2 = "input_r.fastq" 136 #set read2 = "input_r.fastq"
133 #end if 137 #end if
134 ln -s "${input_format.paired.reads.reverse}" "${read2}" && 138 ln -s '${input_format.paired.reads.reverse}' ${read2} &&
135 #else: 139 #else:
136 #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"): 140 #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):
137 #set read1 = "input_f.fastq.gz" 141 #set read1 = "input_f.fastq.gz"
138 #set compressed = "GZ" 142 #set compressed = "GZ"
139 #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"): 143 #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"):
140 #set read1 = "input_f.fastq.bz2" 144 #set read1 = "input_f.fastq.bz2"
141 #set compressed = "BZ2" 145 #set compressed = "BZ2"
142 #else: 146 #else:
143 #set read1 = "input_f.fastq" 147 #set read1 = "input_f.fastq"
144 #end if 148 #end if
145 ln -s "${input_format.paired.reads}" "${read1}" && 149 ln -s '${input_format.paired.reads}' ${read1} &&
146 #end if 150 #end if
147 ]]> 151 ]]>
148 </token> 152 </token>
149 </macros> 153 </macros>