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comparison abyss-pe.xml @ 10:8f1b150a2487 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
author iuc
date Wed, 12 Jan 2022 17:04:56 +0000
parents 890b794c997d
children 7547fcab5d19
comparison
equal deleted inserted replaced
9:890b794c997d 10:8f1b150a2487
1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>de novo sequence assembler</description> 2 <description>de novo sequence assembler</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">abyss</xref> 4 <xref type="bio.tools">abyss</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <token name="@TOOL_VERSION@">2.3.4</token> 7 <token name="@TOOL_VERSION@">2.3.4</token>
8 <token name="@VERSION_SUFFIX@">1</token>
8 <xml name="reads_conditional"> 9 <xml name="reads_conditional">
9 <conditional name="reads"> 10 <conditional name="reads">
10 <param name="reads_selector" type="select" label="Type of paired-end datasets"> 11 <param name="reads_selector" type="select" label="Type of paired-end datasets">
11 <option value="paired">2 separate datasets</option> 12 <option value="paired">2 separate datasets</option>
12 <option value="paired_collection">1 paired dataset collection</option> 13 <option value="paired_collection">1 paired dataset collection</option>
36 <regex match="Error:" /> 37 <regex match="Error:" />
37 <regex match="Exception:" /> 38 <regex match="Exception:" />
38 </stdio> 39 </stdio>
39 <version_command>ABYSS --version | head -n 1</version_command> 40 <version_command>ABYSS --version | head -n 1</version_command>
40 <command><![CDATA[ 41 <command><![CDATA[
42
43 #def get_link_fname($data, $prefix, $index)
44 ## Make a name for symlinked files including extension
45 #return ''.join([str($prefix), '_', str($index), '.', str($data.ext)])
46 #end def
47
48 ## Go through all inputs and create symbolic links
49 #for $i, $v in enumerate($lib_repeat)
50 #if $v.reads.reads_selector == 'paired'
51 ln -s $v.reads.reads1 $get_link_fname($v.reads.reads1, 'lib_reads1', $i) &&
52 ln -s $v.reads.reads2 $get_link_fname($v.reads.reads2, 'lib_reads2', $i) &&
53 #elif $v.reads.reads_selector == 'paired_collection'
54 ln -s $v.reads.reads_coll.forward $get_link_fname($v.reads.reads_coll.forward, 'lib_reads_coll_forward', $i) &&
55 ln -s $v.reads.reads_coll.reverse $get_link_fname($v.reads.reads_coll.reverse, 'lib_reads_coll_reverse', $i) &&
56 #else
57 ln -s $v.reads.reads_il $get_link_fname($v.reads.reads_il, 'lib_reads_il', $i) &&
58 #end if
59 #end for
60
61 #for $i, $v in enumerate($mp_repeat)
62 #if $v.reads.reads_selector == 'paired'
63 ln -s $v.reads.reads1 $get_link_fname($v.reads.reads1, 'mp_reads1', $i) &&
64 ln -s $v.reads.reads2 $get_link_fname($v.reads.reads2, 'mp_reads2', $i) &&
65 #elif $v.reads.reads_selector == 'paired_collection'
66 ln -s $v.reads.reads_coll.forward $get_link_fname($v.reads.reads_coll.forward, 'mp_reads_coll_forward', $i) &&
67 ln -s $v.reads.reads_coll.reverse $get_link_fname($v.reads.reads_coll.reverse, 'mp_reads_coll_reverse', $i) &&
68 #else
69 ln -s $v.reads.reads_il $get_link_fname($v.reads.reads_il, 'mp_reads_il', $i) &&
70 #end if
71 #end for
72
73 #if str($se_reads) != 'None'
74 #for $i, $v in enumerate($se_reads)
75 ln -s $v $get_link_fname($v, 'se_reads', $i) &&
76 #end for
77 #end if
78
79 #if str($long_seqs) != 'None'
80 #for $i, $v in enumerate($long_seqs)
81 ln -s $v $get_link_fname($v, 'long_seqs', $i) &&
82 #end for
83 #end if
84
41 abyss-pe 85 abyss-pe
42 name=abyss 86 name=abyss
43 j=\${GALAXY_SLOTS:-1} 87 j=\${GALAXY_SLOTS:-1}
44 B=\${GALAXY_MEMORY_MB:-2048}M 88 B=\${GALAXY_MEMORY_MB:-2048}M
45 k=$k 89 k=$k
97 #end if 141 #end if
98 #if $N 142 #if $N
99 N='$N' 143 N='$N'
100 #end if 144 #end if
101 #if $lib_repeat 145 #if $lib_repeat
102 lib=' 146 lib='${' '.join(['lib'+str($i) for $i in range(len($lib_repeat))])}'
103 #for $i in range(len($lib_repeat))
104 lib$i
105 #end for
106 '
107 #for $i, $v in enumerate($lib_repeat) 147 #for $i, $v in enumerate($lib_repeat)
108 #if $v.reads.reads_selector == 'paired' 148 #if $v.reads.reads_selector == 'paired'
109 lib${i}='${v.reads.reads1} ${v.reads.reads2}' 149 lib${i}='${get_link_fname($v.reads.reads1, "lib_reads1", $i)} ${get_link_fname($v.reads.reads2, "lib_reads2", $i)}'
110 #elif $v.reads.reads_selector == 'paired_collection' 150 #elif $v.reads.reads_selector == 'paired_collection'
111 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}' 151 lib${i}='$get_link_fname($v.reads.reads_coll.forward, "lib_reads_coll_forward", $i)} ${get_link_fname($v.reads.reads_coll.reverse, "lib_reads_coll_reverse", $i)}'
112 #else 152 #else
113 lib${i}='${v.reads.reads_il}' 153 lib${i}='${get_link_fname($v.reads.reads_il, "lib_reads_il", $i)}'
114 #end if 154 #end if
115 #end for 155 #end for
116 #end if 156 #end if
117 #if str($se_reads) != 'None' 157 #if str($se_reads) != 'None'
118 se=' 158 se='${' '.join([$get_link_fname($v, "se_reads", $i) for $i, $v in enumerate($se_reads)])}'
119 #for $v in $se_reads
120 $v
121 #end for
122 '
123 #end if 159 #end if
124 #if $mp_repeat 160 #if $mp_repeat
125 mp=' 161 mp='${' '.join(['mp'+str($i) for $i in range(len($mp_repeat))])}'
126 #for $i in range(len($mp_repeat))
127 mp$i
128 #end for
129 '
130 #for $i, $v in enumerate($mp_repeat) 162 #for $i, $v in enumerate($mp_repeat)
131 #if $v.reads.reads_selector == 'paired' 163 #if $v.reads.reads_selector == 'paired'
132 mp${i}='${v.reads.reads1} ${v.reads.reads2}' 164 mp${i}='${get_link_fname($v.reads.reads1, "mp_reads1", $i)} ${get_link_fname($v.reads.reads2, "mp_reads2", $i)}'
133 #elif $v.reads.reads_selector == 'paired_collection' 165 #elif $v.reads.reads_selector == 'paired_collection'
134 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}' 166 mp${i}='$get_link_fname($v.reads.reads_coll.forward, "mp_reads_coll_forward", $i)} ${get_link_fname($v.reads.reads_coll.reverse, "mp_reads_coll_reverse", $i)}'
135 #else 167 #else
136 mp${i}='${v.reads.reads_il}' 168 mp${i}='${get_link_fname($v.reads.reads_il, "mp_reads_il", $i)}'
137 #end if 169 #end if
138 #end for 170 #end for
139 #end if 171 #end if
140 #if str($long_seqs) != 'None' 172 #if str($long_seqs) != 'None'
141 long=' 173 long='${' '.join(['long'+str($i) for $i in range(len($long_seqs))])}'
142 #for $i in range(len($long_seqs))
143 long$i
144 #end for
145 '
146 #for $i, $v in enumerate($long_seqs) 174 #for $i, $v in enumerate($long_seqs)
147 long${i}='$v' 175 long$i='${get_link_fname($v, "long_seqs", $i)}'
148 #end for 176 #end for
149 #end if 177 #end if
150 ]]></command> 178 ]]></command>
151 179
152 <inputs> 180 <inputs>
201 <tests> 229 <tests>
202 <test> 230 <test>
203 <repeat name="lib_repeat"> 231 <repeat name="lib_repeat">
204 <conditional name="reads"> 232 <conditional name="reads">
205 <param name="reads_selector" value="paired" /> 233 <param name="reads_selector" value="paired" />
206 <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz" /> 234 <param name="reads1" ftype="fastqsanger.gz" value="assembly_sample-R1.fastq.gz" />
207 <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" /> 235 <param name="reads2" ftype="fastqsanger.gz" value="assembly_sample-R2.fastq.gz" />
208 </conditional> 236 </conditional>
209 </repeat> 237 </repeat>
210 <param name="k" value="50" /> 238 <param name="k" value="50" />
211 <output name="unitigs" file="abyss-unitigs1.fa" /> 239 <output name="unitigs" file="abyss-unitigs1.fa" />
212 <output name="contigs_outfile" file="abyss-contigs1.fa" /> 240 <output name="contigs_outfile" file="abyss-contigs1.fa" />
213 <output name="scaffolds" file="abyss-scaffolds1.fa" /> 241 <output name="scaffolds" file="abyss-scaffolds1.fa" />
214 <output name="indels" file="empty_file.fasta" /> 242 <output name="indels" file="empty_file.fasta" />
215 <output name="stats" file="abyss-stats1.tab" /> 243 <output name="stats" file="abyss-stats1.tab" />
216 </test> 244 </test>
217 <test> 245 <test>
218 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" /> 246 <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
219 <param name="k" value="50" /> 247 <param name="k" value="50" />
220 <output name="unitigs" file="abyss-unitigs2.fa" /> 248 <output name="unitigs" file="abyss-unitigs2.fa" />
221 <output name="indels" file="empty_file.fasta" /> 249 <output name="indels" file="empty_file.fasta" />
222 <output name="stats" file="abyss-stats2.tab" /> 250 <output name="stats" file="abyss-stats2.tab" />
223 </test> 251 </test>
224 <test> 252 <test>
225 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" /> 253 <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" />
226 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" /> 254 <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" />
227 <param name="k" value="50" /> 255 <param name="k" value="50" />
228 <output name="unitigs" file="abyss-unitigs3.fa" /> 256 <output name="unitigs" file="abyss-unitigs3.fa" />
229 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" /> 257 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
230 <output name="indels" file="empty_file.fasta" /> 258 <output name="indels" file="empty_file.fasta" />
231 <output name="stats" file="abyss-stats3.tab" /> 259 <output name="stats" file="abyss-stats3.tab" />