Mercurial > repos > nml > spades
comparison macros.xml @ 15:a39c4cb6ab7f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
author | iuc |
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date | Mon, 24 Jan 2022 18:43:37 +0000 |
parents | 74f20c988994 |
children | 7897763d14ec |
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14:74f20c988994 | 15:a39c4cb6ab7f |
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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 |