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comparison abyss-pe.xml @ 2:2b89471cca20 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
author iuc
date Sun, 01 Sep 2019 11:57:51 -0400
parents 0a5c7992b1ac
children f4fb67b97a63
comparison
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1:0a5c7992b1ac 2:2b89471cca20
1 <tool id="abyss-pe" name="ABySS" version="2.0.1.0"> 1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@">
2 <description>de novo sequence assembler</description> 2 <description>de novo sequence assembler</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.2.1</token>
4 <xml name="reads_conditional"> 5 <xml name="reads_conditional">
5 <conditional name="reads"> 6 <conditional name="reads">
6 <param name="reads_selector" type="select" label="Type of paired-end datasets"> 7 <param name="reads_selector" type="select" label="Type of paired-end datasets">
7 <option value="paired">2 separate datasets</option> 8 <option value="paired">2 separate datasets</option>
8 <option value="paired_collection">1 paired dataset collection</option> 9 <option value="paired_collection">1 paired dataset collection</option>
20 </when> 21 </when>
21 </conditional> 22 </conditional>
22 </xml> 23 </xml>
23 </macros> 24 </macros>
24 <requirements> 25 <requirements>
25 <requirement type="package" version="2.0.1">abyss</requirement> 26 <requirement type="package" version="@TOOL_VERSION@">abyss</requirement>
27 <requirement type="package" version="0.7.17">bwa</requirement>
26 </requirements> 28 </requirements>
27 <stdio> 29 <stdio>
28 <!-- Anything other than zero is an error --> 30 <!-- Anything other than zero is an error -->
29 <exit_code range="1:" /> 31 <exit_code range="1:" />
30 <!-- In case the return code has not been set propery check stderr too --> 32 <!-- In case the return code has not been set propery check stderr too -->
31 <regex match="Error:" /> 33 <regex match="Error:" />
32 <regex match="Exception:" /> 34 <regex match="Exception:" />
33 </stdio> 35 </stdio>
34 <version_command>ABYSS --version | head -n 1</version_command> 36 <version_command>ABYSS --version | head -n 1</version_command>
35 <command> 37 <command>
36 abyss-pe 38 abyss-pe
37 name=abyss 39 name=abyss
38 j=\${GALAXY_SLOTS:-1} 40 j=\${GALAXY_SLOTS:-1}
39 k=$k 41 k=$k
40 42
41 #if str($K) 43 #if str($K)
42 K=$K 44 K=$K
43 #end if 45 #end if
44 #if str($q) 46 #if str($q)
45 q=$q 47 q=$q
46 #end if 48 #end if
47 #if str($Q) 49 #if str($Q)
48 Q=$Q 50 Q=$Q
49 #end if 51 #end if
50 #if str($e) 52 #if str($e)
51 e=$e 53 e=$e
52 #end if 54 #end if
53 #if str($E) 55 #if str($E)
54 E=$E 56 E=$E
55 #end if 57 #end if
56 #if str($t) 58 #if str($t)
57 t=$t 59 t=$t
58 #end if 60 #end if
59 #if str($c) 61 #if str($c)
60 c=$c 62 c=$c
61 #end if 63 #end if
62 #if str($b) 64 #if str($b)
63 b=$b 65 b=$b
64 #end if 66 #end if
65 #if $SS 67 #if $SS
66 SS=--SS 68 SS=--SS
67 #end if 69 #end if
68 #if str($m) 70 #if str($m)
69 m=$m 71 m=$m
70 #end if 72 #end if
71 #if str($p) 73 #if str($p)
72 p=$p 74 p=$p
73 #end if 75 #end if
74 #if str($a) 76 #if str($a)
75 a=$a 77 a=$a
76 #end if 78 #end if
77 #if str($l) 79 #if str($l)
78 l=$l 80 l=$l
79 #end if 81 #end if
80 #if str($s) 82 #if str($s)
81 s=$s 83 s=$s
82 #end if 84 #end if
83 #if str($n) 85 #if str($n)
84 n=$n 86 n=$n
85 #end if 87 #end if
86 #if str($d) 88 #if str($d)
87 d=$d 89 d=$d
88 #end if 90 #end if
89 #if str($S) 91 #if str($S)
90 S=$S 92 S=$S
91 #end if 93 #end if
92 #if str($N) 94 #if str($N)
93 N=$N 95 N=$N
94 #end if 96 #end if
95 #if $lib_repeat 97 #if $lib_repeat
96 lib=' 98 lib='
97 #for $i in range(len($lib_repeat)) 99 #for $i in range(len($lib_repeat))
98 lib$i 100 lib$i
99 #end for 101 #end for
100 ' 102 '
101 #for $i, $v in enumerate($lib_repeat) 103 #for $i, $v in enumerate($lib_repeat)
102 #if $v.reads.reads_selector == 'paired' 104 #if $v.reads.reads_selector == 'paired'
103 lib${i}='${v.reads.reads1} ${v.reads.reads2}' 105 lib${i}='${v.reads.reads1} ${v.reads.reads2}'
104 #elif $v.reads.reads_selector == 'paired_collection' 106 #elif $v.reads.reads_selector == 'paired_collection'
105 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}' 107 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
106 #else 108 #else
107 lib${i}='${v.reads.reads_il}' 109 lib${i}='${v.reads.reads_il}'
108 #end if 110 #end if
109 #end for 111 #end for
110 #end if 112 #end if
111 #if str($se_reads) != 'None' 113 #if str($se_reads) != 'None'
112 se=' 114 se='
113 #for $v in $se_reads 115 #for $v in $se_reads
114 $v 116 $v
115 #end for 117 #end for
116 ' 118 '
117 #end if 119 #end if
118 #if $mp_repeat 120 #if $mp_repeat
119 mp=' 121 mp='
120 #for $i in range(len($mp_repeat)) 122 #for $i in range(len($mp_repeat))
121 mp$i 123 mp$i
122 #end for 124 #end for
123 ' 125 '
124 #for $i, $v in enumerate($mp_repeat) 126 #for $i, $v in enumerate($mp_repeat)
125 #if $v.reads.reads_selector == 'paired' 127 #if $v.reads.reads_selector == 'paired'
126 mp${i}='${v.reads.reads1} ${v.reads.reads2}' 128 mp${i}='${v.reads.reads1} ${v.reads.reads2}'
127 #elif $v.reads.reads_selector == 'paired_collection' 129 #elif $v.reads.reads_selector == 'paired_collection'
128 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}' 130 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
129 #else 131 #else
130 mp${i}='${v.reads.reads_il}' 132 mp${i}='${v.reads.reads_il}'
131 #end if 133 #end if
132 #end for 134 #end for
133 #end if 135 #end if
134 #if str($long_seqs) != 'None' 136 #if str($long_seqs) != 'None'
135 long=' 137 long='
136 #for $i in range(len($long_seqs)) 138 #for $i in range(len($long_seqs))
137 long$i 139 long$i
138 #end for 140 #end for
139 ' 141 '
140 #for $i, $v in enumerate($long_seqs) 142 #for $i, $v in enumerate($long_seqs)
141 long${i}='$v' 143 long${i}='$v'
142 #end for 144 #end for
143 #end if 145 #end if
144 </command> 146 </command>
145 147
146 <inputs> 148 <inputs>
147 <repeat name="lib_repeat" title="Paired-end library" help="(lib)"> 149 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
148 <expand macro="reads_conditional" /> 150 <expand macro="reads_conditional" />
149 </repeat> 151 </repeat>
150 <param name="se_reads" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" help="(se)" /> 152 <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" />
151 <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)"> 153 <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)">
152 <expand macro="reads_conditional" /> 154 <expand macro="reads_conditional" />
153 </repeat> 155 </repeat>
154 <param name="long_seqs" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence (long)" /> 156 <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
155 <param name="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set) (k)" /> 157 <param argument="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set)" />
156 <param name="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional (K)" /> 158 <param argument="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional" />
157 <param name="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value (q)" /> 159 <param argument="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value" />
158 <param name="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N' (Q)" /> 160 <param argument="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N'" />
159 <param name="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median)) (e)" /> 161 <param argument="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median))" />
160 <param name="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0 (E)" /> 162 <param argument="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0" />
161 <param name="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k (t)" /> 163 <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" />
162 <param name="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median) (c)" /> 164 <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />
163 <param name="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles (b)" /> 165 <param argument="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles" />
164 <param name="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced (SS)" /> 166 <param argument="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced" />
165 <param name="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" help="(m)" /> 167 <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" />
166 <param name="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" help="(p)" /> 168 <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
167 <param name="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" help="(a)" /> 169 <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
168 <param name="l" type="integer" value="" min="1" optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k (l)" /> 170 <param argument="l" type="integer" value="" min="1" optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k" />
169 <param name="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value (s)" /> 171 <param argument="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value" />
170 <param name="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" help="(n)" /> 172 <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
171 <param name="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" help="(d)" /> 173 <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
172 <param name="S" type="integer" value="" min="0" optional="true" label="Minimum contig length required for building scaffolds (in bp)" help="Defaults to the value of s (S)" /> 174 <param argument="S" type="integer" value="" min="0" optional="true" label="Minimum contig length required for building scaffolds (in bp)" help="Defaults to the value of s" />
173 <param name="N" type="integer" value="" min="0" optional="true" label="Minimum number of pairs required for building scaffolds" help="Defaults to the value of n (N)" /> 175 <param argument="N" type="integer" value="" min="0" optional="true" label="Minimum number of pairs required for building scaffolds" help="Defaults to the value of n" />
174 </inputs> 176 </inputs>
175 177
176 <outputs> 178 <outputs>
177 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" /> 179 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />
178 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa"> 180 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">