Mercurial > repos > iuc > spades_metaplasmidspades

comparison macros.xml @ 1:0ec2f2969a3a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
author iuc
date Mon, 24 Jan 2022 18:46:12 +0000
parents 32ab23671cc1
children b8002c3f7141
comparison
equal deleted inserted replaced
0:32ab23671cc1 1:0ec2f2969a3a
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.15.3</token> 2 <token name="@TOOL_VERSION@">3.15.3</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
7 <requirement type="package" version="3.0">zip</requirement> 7 <requirement type="package" version="3.0">zip</requirement>
8 <yield/> 8 <yield/>
52 #set file_paths1 = [] 52 #set file_paths1 = []
53 #for $input_file in $singlePaired.input1 53 #for $input_file in $singlePaired.input1
54 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 54 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
55 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 55 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
56 #set $file_path = 'reads1/' + $fname 56 #set $file_path = 'reads1/' + $fname
57 ln -s '$input_file' $file_path && 57 ln -s '$input_file' '$file_path' &&
58 $file_paths1.append($file_path) 58 $file_paths1.append($file_path)
59 #end for 59 #end for
60 #else if $singlePaired.sPaired == "paired" 60 #else if $singlePaired.sPaired == "paired"
61 mkdir -p paired_reads1 && 61 mkdir -p paired_reads1 &&
62 #set fw_reads1 = [] 62 #set fw_reads1 = []
63 #for $input_file in $singlePaired.input1 63 #for $input_file in $singlePaired.input1
64 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 64 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
65 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 65 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
66 #set $file_path = 'paired_reads1/' + str($fname) 66 #set $file_path = 'paired_reads1/' + str($fname)
67 ln -s '$input_file' $file_path && 67 ln -s '$input_file' '$file_path' &&
68 $fw_reads1.append($file_path) 68 $fw_reads1.append($file_path)
69 #end for 69 #end for
70 #set rv_reads1 = [] 70 #set rv_reads1 = []
71 #for $input_file in $singlePaired.input2 71 #for $input_file in $singlePaired.input2
72 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 72 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
73 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 73 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
74 #set $file_path = 'paired_reads1/' + str($fname) 74 #set $file_path = 'paired_reads1/' + str($fname)
75 ln -s '$input_file' $file_path && 75 ln -s '$input_file' '$file_path' &&
76 $rv_reads1.append($file_path) 76 $rv_reads1.append($file_path)
77 #end for 77 #end for
78 #silent $fw_reads1.sort() 78 #silent $fw_reads1.sort()
79 #silent $rv_reads1.sort() 79 #silent $rv_reads1.sort()
80 #else 80 #else
82 #set fw_reads1 = [] 82 #set fw_reads1 = []
83 #set rv_reads1 = [] 83 #set rv_reads1 = []
84 #for $i, $input_file in enumerate($singlePaired.input) 84 #for $i, $input_file in enumerate($singlePaired.input)
85 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq') 85 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
86 #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext 86 #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext
87 ln -s '$input_file.forward' $file_path && 87 ln -s '$input_file.forward' '$file_path' &&
88 $fw_reads1.append($file_path) 88 $fw_reads1.append($file_path)
89 #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext 89 #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext
90 ln -s '$input_file.reverse' $file_path && 90 ln -s '$input_file.reverse' '$file_path' &&
91 $rv_reads1.append($file_path) 91 $rv_reads1.append($file_path)
92 #end for 92 #end for
93 #end if 93 #end if
94 ]]></token> 94 ]]></token>
95 95
99 #set file_paths2 = [] 99 #set file_paths2 = []
100 #for $input_file in $additional_reads.singlePaired.input1 100 #for $input_file in $additional_reads.singlePaired.input1
101 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 101 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
102 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 102 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
103 #set $file_path = 'reads2/' + $fname 103 #set $file_path = 'reads2/' + $fname
104 ln -s '$input_file' $file_path && 104 ln -s '$input_file' '$file_path' &&
105 $file_paths2.append($file_path) 105 $file_paths2.append($file_path)
106 #end for 106 #end for
107 #else if $additional_reads.singlePaired.sPaired == "paired" 107 #else if $additional_reads.singlePaired.sPaired == "paired"
108 mkdir -p paired_reads2 && 108 mkdir -p paired_reads2 &&
109 #set fw_reads2 = [] 109 #set fw_reads2 = []
110 #for $input_file in $additional_reads.singlePaired.input1 110 #for $input_file in $additional_reads.singlePaired.input1
111 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 111 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
112 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 112 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
113 #set $file_path = 'paired_reads2/' + str($fname) 113 #set $file_path = 'paired_reads2/' + str($fname)
114 ln -s '$input_file' $file_path && 114 ln -s '$input_file' '$file_path' &&
115 $fw_reads2.append($file_path) 115 $fw_reads2.append($file_path)
116 #end for 116 #end for
117 #set rv_reads2 = [] 117 #set rv_reads2 = []
118 #for $input_file in $additional_reads.singlePaired.input2 118 #for $input_file in $additional_reads.singlePaired.input2
119 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 119 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
120 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext 120 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
121 #set $file_path = 'paired_reads2/' + str($fname) 121 #set $file_path = 'paired_reads2/' + str($fname)
122 ln -s '$input_file' $file_path && 122 ln -s '$input_file' '$file_path' &&
123 $rv_reads2.append($file_path) 123 $rv_reads2.append($file_path)
124 #end for 124 #end for
125 #silent $fw_reads2.sort() 125 #silent $fw_reads2.sort()
126 #silent $rv_reads2.sort() 126 #silent $rv_reads2.sort()
127 #else 127 #else
129 #set fw_reads2 = [] 129 #set fw_reads2 = []
130 #set rv_reads2 = [] 130 #set rv_reads2 = []
131 #for $i, $input_file in enumerate($additional_reads.singlePaired.input) 131 #for $i, $input_file in enumerate($additional_reads.singlePaired.input)
132 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq') 132 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
133 #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext 133 #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext
134 ln -s '$input_file.forward' $file_path && 134 ln -s '$input_file.forward' '$file_path' &&
135 $fw_reads2.append($file_path) 135 $fw_reads2.append($file_path)
136 #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext 136 #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext
137 ln -s '$input_file.reverse' $file_path && 137 ln -s '$input_file.reverse' '$file_path' &&
138 $rv_reads2.append($file_path) 138 $rv_reads2.append($file_path)
139 #end for 139 #end for
140 #end if 140 #end if
141 ]]></token> 141 ]]></token>
142 142
233 #set trusted_contigs = [] 233 #set trusted_contigs = []
234 #for $i, $input_file in enumerate($arf.trusted_contigs,1) 234 #for $i, $input_file in enumerate($arf.trusted_contigs,1)
235 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 235 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
236 #set $fname = 'file' + str($i) + '.' + $ext 236 #set $fname = 'file' + str($i) + '.' + $ext
237 #set $file_path = 'trusted_contigs/' + $fname 237 #set $file_path = 'trusted_contigs/' + $fname
238 ln -s '$input_file' $file_path && 238 ln -s '$input_file' '$file_path' &&
239 $trusted_contigs.append($file_path) 239 $trusted_contigs.append($file_path)
240 #end for 240 #end for
241 #end if 241 #end if
242 #if $arf.untrusted_contigs 242 #if $arf.untrusted_contigs
243 mkdir -p untrusted_contigs && 243 mkdir -p untrusted_contigs &&
244 #set untrusted_contigs = [] 244 #set untrusted_contigs = []
245 #for $i, $input_file in enumerate($arf.untrusted_contigs,1) 245 #for $i, $input_file in enumerate($arf.untrusted_contigs,1)
246 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 246 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
247 #set $fname = 'file' + str($i) + '.' + $ext 247 #set $fname = 'file' + str($i) + '.' + $ext
248 #set $file_path = 'untrusted_contigs/' + $fname 248 #set $file_path = 'untrusted_contigs/' + $fname
249 ln -s '$input_file' $file_path && 249 ln -s '$input_file' '$file_path' &&
250 $untrusted_contigs.append($file_path) 250 $untrusted_contigs.append($file_path)
251 #end for 251 #end for
252 #end if 252 #end if
253 ]]></token> 253 ]]></token>
254 254
258 #set nanopore_reads = [] 258 #set nanopore_reads = []
259 #for $i, $input_file in enumerate($arf.nanopore,1) 259 #for $i, $input_file in enumerate($arf.nanopore,1)
260 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 260 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
261 #set $fname = 'file' + str($i) + '.' + $ext 261 #set $fname = 'file' + str($i) + '.' + $ext
262 #set $file_path = 'nanopore_reads/' + $fname 262 #set $file_path = 'nanopore_reads/' + $fname
263 ln -s '$input_file' $file_path && 263 ln -s '$input_file' '$file_path' &&
264 $nanopore_reads.append($file_path) 264 $nanopore_reads.append($file_path)
265 #end for 265 #end for
266 #end if 266 #end if
267 #if $arf.pacbio 267 #if $arf.pacbio
268 mkdir -p pacbio_reads && 268 mkdir -p pacbio_reads &&
269 #set pacbio_reads = [] 269 #set pacbio_reads = []
270 #for $i, $input_file in enumerate($arf.pacbio,1) 270 #for $i, $input_file in enumerate($arf.pacbio,1)
271 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 271 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
272 #set $fname = 'file' + str($i) + '.' + $ext 272 #set $fname = 'file' + str($i) + '.' + $ext
273 #set $file_path = 'pacbio_reads/' + $fname 273 #set $file_path = 'pacbio_reads/' + $fname
274 ln -s '$input_file' $file_path && 274 ln -s '$input_file' '$file_path' &&
275 $pacbio_reads.append($file_path) 275 $pacbio_reads.append($file_path)
276 #end for 276 #end for
277 #end if 277 #end if
278 ]]></token> 278 ]]></token>
279 279
283 #set sanger_reads = [] 283 #set sanger_reads = []
284 #for $i, $input_file in enumerate($arf.sanger,1) 284 #for $i, $input_file in enumerate($arf.sanger,1)
285 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 285 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
286 #set $fname = 'file' + str($i) + '.' + $ext 286 #set $fname = 'file' + str($i) + '.' + $ext
287 #set $file_path = 'sanger_reads/' + $fname 287 #set $file_path = 'sanger_reads/' + $fname
288 ln -s '$input_file' $file_path && 288 ln -s '$input_file' '$file_path' &&
289 $sanger_reads.append($file_path) 289 $sanger_reads.append($file_path)
290 #end for 290 #end for
291 #end if 291 #end if
292 ]]></token> 292 ]]></token>
293 293
297 #set flrna_reads = [] 297 #set flrna_reads = []
298 #for $i, $input_file in enumerate($arf.flrna,1) 298 #for $i, $input_file in enumerate($arf.flrna,1)
299 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq') 299 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
300 #set $fname = 'file' + str($i) + '.' + $ext 300 #set $fname = 'file' + str($i) + '.' + $ext
301 #set $file_path = 'flrna_reads/' + $fname 301 #set $file_path = 'flrna_reads/' + $fname
302 ln -s '$input_file' $file_path && 302 ln -s '$input_file' '$file_path' &&
303 $flrna_reads.append($file_path) 303 $flrna_reads.append($file_path)
304 #end for 304 #end for
305 #end if 305 #end if
306 ]]></token> 306 ]]></token>
307 307
311 #set assembly_graphs = [] 311 #set assembly_graphs = []
312 #for $i, $input_file in enumerate($arf.assembly_graph,1) 312 #for $i, $input_file in enumerate($arf.assembly_graph,1)
313 #set $ext = $input_file.ext.replace('gfa1', 'gfa') 313 #set $ext = $input_file.ext.replace('gfa1', 'gfa')
314 #set $fname = 'file' + str($i) + '.' + $ext 314 #set $fname = 'file' + str($i) + '.' + $ext
315 #set $file_path = 'assembly_graphs/' + $fname 315 #set $file_path = 'assembly_graphs/' + $fname
316 ln -s '$input_file' $file_path && 316 ln -s '$input_file' '$file_path' &&
317 $assembly_graphs.append($file_path) 317 $assembly_graphs.append($file_path)
318 #end for 318 #end for
319 #end if 319 #end if
320 ]]></token> 320 ]]></token>
321 321