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

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
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1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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1 <tool id="abyss-pe" name="ABySS" version="2.0.1.0">
0
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2 <description>de novo sequence assembler</description>
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3 <macros>
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4 <xml name="reads_conditional">
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5 <conditional name="reads">
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6 <param name="reads_selector" type="select" label="Type of paired-end datasets">
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7 <option value="paired">2 separate datasets</option>
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8 <option value="paired_collection">1 paired dataset collection</option>
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9 <option value="paired_il">1 dataset of interleaved reads</option>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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10 </param>
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11 <when value="paired">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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12 <param name="reads1" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 1" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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13 <param name="reads2" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 2" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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14 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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15 <when value="paired_collection">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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16 <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" />
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17 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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18 <when value="paired_il">
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19 <param name="reads_il" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Interleaved paired-end reads" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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20 </when>
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21 </conditional>
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22 </xml>
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23 </macros>
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24 <requirements>
1
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25 <requirement type="package" version="2.0.1">abyss</requirement>
0
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26 </requirements>
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27 <stdio>
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28 <!-- Anything other than zero is an error -->
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29 <exit_code range="1:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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30 <!-- In case the return code has not been set propery check stderr too -->
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31 <regex match="Error:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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32 <regex match="Exception:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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33 </stdio>
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34 <version_command>ABYSS --version | head -n 1</version_command>
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35 <command>
1
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36 abyss-pe
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37 name=abyss
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38 j=\${GALAXY_SLOTS:-1}
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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39 k=$k
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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40
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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41 #if str($K)
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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42 K=$K
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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43 #end if
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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44 #if str($q)
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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45 q=$q
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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46 #end if
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
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47 #if str($Q)
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48 Q=$Q
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49 #end if
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50 #if str($e)
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51 e=$e
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52 #end if
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53 #if str($E)
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54 E=$E
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55 #end if
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56 #if str($t)
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57 t=$t
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58 #end if
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59 #if str($c)
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60 c=$c
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61 #end if
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62 #if str($b)
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63 b=$b
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64 #end if
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65 #if $SS
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66 SS=--SS
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67 #end if
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68 #if str($m)
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69 m=$m
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70 #end if
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71 #if str($p)
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72 p=$p
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73 #end if
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74 #if str($a)
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75 a=$a
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76 #end if
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77 #if str($l)
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78 l=$l
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79 #end if
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80 #if str($s)
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81 s=$s
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82 #end if
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83 #if str($n)
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84 n=$n
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85 #end if
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86 #if str($d)
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87 d=$d
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88 #end if
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89 #if str($S)
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90 S=$S
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91 #end if
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92 #if str($N)
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93 N=$N
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94 #end if
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95 #if $lib_repeat
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96 lib='
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97 #for $i in range(len($lib_repeat))
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98 lib$i
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99 #end for
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100 '
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101 #for $i, $v in enumerate($lib_repeat)
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102 #if $v.reads.reads_selector == 'paired'
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103 lib${i}='${v.reads.reads1} ${v.reads.reads2}'
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104 #elif $v.reads.reads_selector == 'paired_collection'
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105 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
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106 #else
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107 lib${i}='${v.reads.reads_il}'
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108 #end if
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109 #end for
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110 #end if
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111 #if str($se_reads) != 'None'
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112 se='
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113 #for $v in $se_reads
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114 $v
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115 #end for
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116 '
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117 #end if
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118 #if $mp_repeat
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119 mp='
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120 #for $i in range(len($mp_repeat))
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121 mp$i
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122 #end for
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123 '
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124 #for $i, $v in enumerate($mp_repeat)
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125 #if $v.reads.reads_selector == 'paired'
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126 mp${i}='${v.reads.reads1} ${v.reads.reads2}'
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127 #elif $v.reads.reads_selector == 'paired_collection'
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128 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
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129 #else
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130 mp${i}='${v.reads.reads_il}'
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131 #end if
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132 #end for
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133 #end if
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134 #if str($long_seqs) != 'None'
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135 long='
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136 #for $i in range(len($long_seqs))
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137 long$i
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138 #end for
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139 '
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140 #for $i, $v in enumerate($long_seqs)
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141 long${i}='$v'
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142 #end for
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143 #end if
0
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144 </command>
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145
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146 <inputs>
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147 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
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148 <expand macro="reads_conditional" />
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149 </repeat>
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150 <param name="se_reads" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" help="(se)" />
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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)">
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152 <expand macro="reads_conditional" />
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153 </repeat>
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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)" />
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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)" />
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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)" />
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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)" />
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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)" />
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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)" />
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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)" />
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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)" />
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162 <param name="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median) (c)" />
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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)" />
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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)" />
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165 <param name="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" help="(m)" />
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166 <param name="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" help="(p)" />
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167 <param name="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" help="(a)" />
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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)" />
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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)" />
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170 <param name="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" help="(n)" />
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171 <param name="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" help="(d)" />
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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)" />
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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)" />
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174 </inputs>
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175
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176 <outputs>
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177 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />
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178 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">
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179 <filter>lib_repeat</filter>
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180 </data>
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181 <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">
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182 <filter>lib_repeat or mp_repeat</filter>
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183 </data>
1
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184 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
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185 <filter>long_seqs</filter>
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186 </data>
0
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187 <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
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188 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
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189 <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
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190 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
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191 </outputs>
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192
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193 <tests>
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194 <test>
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195 <repeat name="lib_repeat">
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196 <conditional name="reads">
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197 <param name="reads_selector" value="paired" />
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198 <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq" />
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199 <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
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200 </conditional>
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201 </repeat>
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202 <param name="k" value="50" />
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203 <output name="unitigs" file="abyss-unitigs1.fa" />
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204 <output name="contigs_outfile" file="abyss-contigs1.fa" />
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205 <output name="scaffolds" file="abyss-scaffolds1.fa" />
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206 <output name="bubbles" file="empty_file.fasta" />
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207 <output name="indels" file="empty_file.fasta" />
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208 <output name="coverage_histogram_outfile" file="coverage1.hist" />
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209 <output name="stats" file="abyss-stats1.tab" />
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210 </test>
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211 <test>
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212 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
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213 <param name="k" value="50" />
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214 <output name="unitigs" file="abyss-unitigs2.fa" />
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215 <output name="bubbles" file="empty_file.fasta" />
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216 <output name="indels" file="empty_file.fasta" />
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217 <output name="coverage_histogram_outfile" file="coverage2.hist" />
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218 <output name="stats" file="abyss-stats2.tab" />
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219 </test>
1
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220 <test>
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221 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
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222 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
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223 <param name="k" value="50" />
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224 <output name="unitigs" file="abyss-unitigs3.fa" />
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225 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
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226 <output name="bubbles" file="empty_file.fasta" />
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227 <output name="indels" file="empty_file.fasta" />
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228 <output name="coverage_histogram_outfile" file="coverage3.hist" />
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229 <output name="stats" file="abyss-stats3.tab" />
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230 </test>
0
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231 </tests>
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232 <help>
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233 **What it does**
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234
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235 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
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236
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237 **Input**
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238
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239 Input files should be FASTA or FASTQ files.
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240
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241 For paired reads, a pair of reads must be named with the suffixes /1 and /2 to identify the first and second read, or the reads may be named identically. The paired reads may be in separate files or interleaved in a single file.
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242
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243 At least a paired-end library or a single-end library must be provided.
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244
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245 Contigs are generated only if at least a paired-end library is provided. Scaffolds are generated only if at least a paired-end library or a mate-pair library is provided.
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246
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247 **Description**
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248
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249 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf .
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250
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251 **License and citation**
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252
1
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253 This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
0
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254
1
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255 .. _Earlham Institute: http://www.earlham.ac.uk/
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256 .. _MIT license: https://opensource.org/licenses/MIT
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257
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258 You can use this tool only if you agree to the license terms of: `ABySS`_.
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259
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260 .. _ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss
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261 </help>
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262 <citations>
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263 <citation type="doi">10.1101/gr.089532.108</citation>
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264 </citations>
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265 </tool>