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comparison abyss-pe.xml @ 1:0a5c7992b1ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
author iuc
date Wed, 01 Mar 2017 15:17:12 -0500
parents f048033da666
children 2b89471cca20
comparison
equal deleted inserted replaced
0:f048033da666 1:0a5c7992b1ac
1 <tool id="abyss-pe" name="ABySS" version="1.9.0.0"> 1 <tool id="abyss-pe" name="ABySS" version="2.0.1.0">
2 <description>de novo sequence assembler</description> 2 <description>de novo sequence assembler</description>
3 <macros> 3 <macros>
4 <xml name="reads_conditional"> 4 <xml name="reads_conditional">
5 <conditional name="reads"> 5 <conditional name="reads">
6 <param name="reads_selector" type="select" label="Type of paired-end datasets"> 6 <param name="reads_selector" type="select" label="Type of paired-end datasets">
20 </when> 20 </when>
21 </conditional> 21 </conditional>
22 </xml> 22 </xml>
23 </macros> 23 </macros>
24 <requirements> 24 <requirements>
25 <requirement type="package" version="1.9.0">abyss</requirement> 25 <requirement type="package" version="2.0.1">abyss</requirement>
26 </requirements> 26 </requirements>
27 <stdio> 27 <stdio>
28 <!-- Anything other than zero is an error --> 28 <!-- Anything other than zero is an error -->
29 <exit_code range="1:" /> 29 <exit_code range="1:" />
30 <!-- In case the return code has not been set propery check stderr too --> 30 <!-- In case the return code has not been set propery check stderr too -->
31 <regex match="Error:" /> 31 <regex match="Error:" />
32 <regex match="Exception:" /> 32 <regex match="Exception:" />
33 </stdio> 33 </stdio>
34 <version_command>ABYSS --version | head -n 1</version_command> 34 <version_command>ABYSS --version | head -n 1</version_command>
35 <command> 35 <command>
36 abyss-pe name=abyss j=\${GALAXY_SLOTS:-1} k=$k 36 abyss-pe
37 #if str($K) 37 name=abyss
38 K=$K 38 j=\${GALAXY_SLOTS:-1}
39 #end if 39 k=$k
40 #if str($q) 40
41 q=$q 41 #if str($K)
42 #end if 42 K=$K
43 #if str($Q) 43 #end if
44 Q=$Q 44 #if str($q)
45 #end if 45 q=$q
46 #if str($e) 46 #end if
47 e=$e 47 #if str($Q)
48 #end if 48 Q=$Q
49 #if str($E) 49 #end if
50 E=$E 50 #if str($e)
51 #end if 51 e=$e
52 #if str($t) 52 #end if
53 t=$t 53 #if str($E)
54 #end if 54 E=$E
55 #if str($c) 55 #end if
56 c=$c 56 #if str($t)
57 #end if 57 t=$t
58 #if str($b) 58 #end if
59 b=$b 59 #if str($c)
60 #end if 60 c=$c
61 #if $SS 61 #end if
62 SS=--SS 62 #if str($b)
63 #end if 63 b=$b
64 #if str($m) 64 #end if
65 m=$m 65 #if $SS
66 #end if 66 SS=--SS
67 #if str($p) 67 #end if
68 p=$p 68 #if str($m)
69 #end if 69 m=$m
70 #if str($a) 70 #end if
71 a=$a 71 #if str($p)
72 #end if 72 p=$p
73 #if str($l) 73 #end if
74 l=$l 74 #if str($a)
75 #end if 75 a=$a
76 #if str($s) 76 #end if
77 s=$s 77 #if str($l)
78 #end if 78 l=$l
79 #if str($n) 79 #end if
80 n=$n 80 #if str($s)
81 #end if 81 s=$s
82 #if str($d) 82 #end if
83 d=$d 83 #if str($n)
84 #end if 84 n=$n
85 #if str($S) 85 #end if
86 S=$S 86 #if str($d)
87 #end if 87 d=$d
88 #if str($N) 88 #end if
89 N=$N 89 #if str($S)
90 #end if 90 S=$S
91 #if $lib_repeat 91 #end if
92 lib=' 92 #if str($N)
93 #for $i in range(len($lib_repeat)) 93 N=$N
94 lib$i 94 #end if
95 #end for 95 #if $lib_repeat
96 ' 96 lib='
97 #for $i, $v in enumerate($lib_repeat) 97 #for $i in range(len($lib_repeat))
98 #if $v.reads.reads_selector == 'paired' 98 lib$i
99 lib${i}='${v.reads.reads1} ${v.reads.reads2}' 99 #end for
100 #elif $v.reads.reads_selector == 'paired_collection' 100 '
101 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}' 101 #for $i, $v in enumerate($lib_repeat)
102 #else 102 #if $v.reads.reads_selector == 'paired'
103 lib${i}='${v.reads.reads_il}' 103 lib${i}='${v.reads.reads1} ${v.reads.reads2}'
104 #end if 104 #elif $v.reads.reads_selector == 'paired_collection'
105 #end for 105 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
106 #end if 106 #else
107 #if str($se_reads) != 'None' 107 lib${i}='${v.reads.reads_il}'
108 se=' 108 #end if
109 #for $v in $se_reads 109 #end for
110 $v 110 #end if
111 #end for 111 #if str($se_reads) != 'None'
112 ' 112 se='
113 #end if 113 #for $v in $se_reads
114 #if $mp_repeat 114 $v
115 mp=' 115 #end for
116 #for $i in range(len($mp_repeat)) 116 '
117 mp$i 117 #end if
118 #end for 118 #if $mp_repeat
119 ' 119 mp='
120 #for $i, $v in enumerate($mp_repeat) 120 #for $i in range(len($mp_repeat))
121 #if $v.reads.reads_selector == 'paired' 121 mp$i
122 mp${i}='${v.reads.reads1} ${v.reads.reads2}' 122 #end for
123 #elif $v.reads.reads_selector == 'paired_collection' 123 '
124 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}' 124 #for $i, $v in enumerate($mp_repeat)
125 #else 125 #if $v.reads.reads_selector == 'paired'
126 mp${i}='${v.reads.reads_il}' 126 mp${i}='${v.reads.reads1} ${v.reads.reads2}'
127 #end if 127 #elif $v.reads.reads_selector == 'paired_collection'
128 #end for 128 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
129 #end if 129 #else
130 #if str($long_seqs) != 'None' 130 mp${i}='${v.reads.reads_il}'
131 long=' 131 #end if
132 #for $v in $long_seqs 132 #end for
133 $v 133 #end if
134 #end for 134 #if str($long_seqs) != 'None'
135 ' 135 long='
136 #end if 136 #for $i in range(len($long_seqs))
137 long$i
138 #end for
139 '
140 #for $i, $v in enumerate($long_seqs)
141 long${i}='$v'
142 #end for
143 #end if
137 </command> 144 </command>
138 145
139 <inputs> 146 <inputs>
140 <repeat name="lib_repeat" title="Paired-end library" help="(lib)"> 147 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
141 <expand macro="reads_conditional" /> 148 <expand macro="reads_conditional" />
172 <filter>lib_repeat</filter> 179 <filter>lib_repeat</filter>
173 </data> 180 </data>
174 <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa"> 181 <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">
175 <filter>lib_repeat or mp_repeat</filter> 182 <filter>lib_repeat or mp_repeat</filter>
176 </data> 183 </data>
184 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
185 <filter>long_seqs</filter>
186 </data>
177 <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" /> 187 <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
178 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" /> 188 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
179 <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" /> 189 <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
180 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" /> 190 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
181 </outputs> 191 </outputs>
205 <output name="bubbles" file="empty_file.fasta" /> 215 <output name="bubbles" file="empty_file.fasta" />
206 <output name="indels" file="empty_file.fasta" /> 216 <output name="indels" file="empty_file.fasta" />
207 <output name="coverage_histogram_outfile" file="coverage2.hist" /> 217 <output name="coverage_histogram_outfile" file="coverage2.hist" />
208 <output name="stats" file="abyss-stats2.tab" /> 218 <output name="stats" file="abyss-stats2.tab" />
209 </test> 219 </test>
220 <test>
221 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
222 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
223 <param name="k" value="50" />
224 <output name="unitigs" file="abyss-unitigs3.fa" />
225 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
226 <output name="bubbles" file="empty_file.fasta" />
227 <output name="indels" file="empty_file.fasta" />
228 <output name="coverage_histogram_outfile" file="coverage3.hist" />
229 <output name="stats" file="abyss-stats3.tab" />
230 </test>
210 </tests> 231 </tests>
211 <help> 232 <help>
212 **What it does** 233 **What it does**
213 234
214 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes. 235 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
227 248
228 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf . 249 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf .
229 250
230 **License and citation** 251 **License and citation**
231 252
232 This Galaxy tool is Copyright © 2015 `The Genome Analysis Centre (TGAC)`_ and is released under the `MIT license`_. 253 This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
233 254
234 .. _The Genome Analysis Centre (TGAC): http://www.tgac.ac.uk/ 255 .. _Earlham Institute: http://www.earlham.ac.uk/
235 .. _MIT license: http://opensource.org/licenses/MIT 256 .. _MIT license: https://opensource.org/licenses/MIT
236 257
237 You can use this tool only if you agree to the license terms of: `ABySS`_. 258 You can use this tool only if you agree to the license terms of: `ABySS`_.
238 259
239 .. _ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss 260 .. _ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss
240 </help> 261 </help>