Mercurial > repos > rnateam > segemehl

annotate segemehl.xml @ 5:9c0d4ec99ba9 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author rnateam
date Thu, 27 Sep 2018 06:31:11 -0400
parents db367d012fa3
children
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5
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
rnateam
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1 <tool id="segemehl" name="segemehl" version="0.2.0.4">
4
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2 <description>short read mapping with gaps</description>
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3 <requirements>
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4 <requirement type="package" version="0.2.0">segemehl</requirement>
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5 </requirements>
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6 <stdio>
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7 <regex match="Exit forced"
3
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8 source="both"
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9 level="fatal"
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10 description="Execution halted." />
4
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11 </stdio>
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12 <command>
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13 <!--
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14 ## check for single/pair-end
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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15 #if str( $library.type ) == "single":
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16 #set $query_list = list()
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17 ## prepare inputs
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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18 #for $fastq in $library.input_query:
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19 $query_list.append('%s' % $fastq )
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20 #end for
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21 -q "#echo ' '.join( $query_list )#"
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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22 #else
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23 ## prepare inputs
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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24 #set $mate1 = list()
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25 #set $mate2 = list()
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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26 #for $mate_pair in $library.mate_list:
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27 $mate1.append( str($mate_pair.first_strand_query) )
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28 $mate2.append( str($mate_pair.second_strand_query) )
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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29 #end for
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30
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31 -q #echo ','.join($mate1)
9c0d4ec99ba9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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32 -p #echo ','.join($mate2)
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33
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34 -I $library.maxinsertsize
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35 #end if
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36 -->
4
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37 <![CDATA[
5
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38 ## UNIMPLEMENTED
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39 ## [SEEDEXTENSIONPARAMS]
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40 ## -e, --extensionscore <n> score of a match during extension (default:2)
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41 ## -n, --extensionpenalty <n> penalty for a mismatch during extension (default:4)
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42 ## -X, --dropoff <n> dropoff parameter for extension (default:8)
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43 ## --showalign
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44
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45 ## prepare segemehl index if no reference genome is supplied
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46 #if $refGenomeSource.genomeSource == "history":
3
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47 mkdir ./temp_index/ &&
4
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48 #set $temp_index = './temp_index/temp.idx'
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49 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome &&
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50 #else:
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51 #set $temp_index = $refGenomeSource.index.fields.index_path
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52 #end if
4
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53
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54 ## execute segemehl
4
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55 segemehl.x
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56
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57 ## number of threads
4
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58 -t "\${GALAXY_SLOTS:-12}"
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59
3
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60 #if $refGenomeSource.genomeSource == "history":
4
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61 -d $refGenomeSource.own_reference_genome
3
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62 #else:
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63 -d ${refGenomeSource.index.fields.db_path}
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64 #end if
4
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65
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66 -i $temp_index
4
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67
0
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68 ## check for single/pair-end
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69 #if str( $library.type ) == "single":
5
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70 ## prepare inputs
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71 -q ${library.input_query}
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72 #else
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73 -q ${mate_pair.first_strand_query}
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74 -p ${mate_pair.second_strand_query}
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75 -I ${library.maxinsertsize}
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76 #end if
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77 #if str( $bisulfite ) != "0":
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78 -F $bisulfite
0
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79 #end if
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80 -m $minsize
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81 -A $accuracy
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82 -H $hitstrategy
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83 #if str( $prime5 ).strip():
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84 -P "$prime5"
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85 #end if
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86 #if str( $prime3 ).strip():
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87 -Q "$prime3"
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88 #end if
5
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89 -R $clipacc
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90 $polyA
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91 $autoclip
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92 $hardclip
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93 $order
3
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94 #if $maxout:
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95 --maxout $maxout
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96 #end if
4
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97 #if str( $splitreads.splits ) == "splits":
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98 --splits
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99 --minsplicecover $splitreads.minsplicecover
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100 --minfragscore $splitreads.minfragscore
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101 --minfraglen $splitreads.minfraglen
5
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102 --splicescorescale $splitreads.splicescorescale
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103 --maxsplitevalue $splitreads.maxsplitevalue
4
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104 #end if
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105 -M $maxinterval
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106 -E $evalue
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107 -D $differences
5
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108 -J $jump
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109 -s
3
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110 -o '$segemehl_out'
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111 #if str( $nomatchfilename ) == 'yes':
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112 -u '$segemehl_outunmatched'
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113 #end if
4
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114 ]]>
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115 </command>
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116 <inputs>
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117 <conditional name="refGenomeSource">
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118 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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119 <option value="indexed">Use a built-in index</option>
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120 <option value="history">Use one from the history</option>
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121 </param>
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122 <when value="indexed">
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123 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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124 <options from_data_table="segemehl_indexes">
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125 <column name="value" index="0"/>
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126 <column name="dbkey" index="1"/>
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127 <column name="name" index="2"/>
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128 <column name="db_path" index="3"/>
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129 <column name="index_path" index="4"/>
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130 <filter type="sort_by" column="2"/>
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131 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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132 </options>
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133 </param>
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134 </when> <!-- build-in -->
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135 <when value="history">
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136 <param name="own_reference_genome" type="data" format="fasta" label="Select the reference genome" />
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137 </when> <!-- history -->
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138 </conditional> <!-- refGenomeSource -->
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139
4
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140 <conditional name="library">
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141 <param name="type" type="select" label="Is this library paired-end?">
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142 <option value="single">Single-end</option>
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143 <option value="paired">Paired-end</option>
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144 </param>
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145 <when value="single">
5
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146 <!-- <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" /> -->
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147 <param name="input_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" />
4
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148 </when>
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149 <when value="paired">
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150 <!-- ToDo paired coolections -->
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151 <repeat name="mate_list" title="Paired End Pairs" min="1">
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152 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" />
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153 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" />
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154 </repeat>
5
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155 <param argument="--maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000" />
4
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156 </when>
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157 </conditional>
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158
4
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159 <conditional name="splitreads">
5
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160 <param argument="splits" type="select" label="Detect split/spliced reads">
4
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161 <option value="nosplit">No splits</option>
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162 <option value="splits">Split reads</option>
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163 </param>
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164 <when value="splits">
5
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165 <param argument="--minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" />
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166 <param argument="--minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" />
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167 <param argument="--minfraglen" type="integer" value="20" label="Min length of a spliced fragment" />
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168 <param argument="--splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score"
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169 help="Report only if this value x score is larger than next best spliced alignment" />
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170 <param argument="--maxsplitevalue" type="float" min="0" value="50.000000" label="max evalue for splits"/>
4
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171 </when>
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172 <when value="nosplit">
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173 </when>
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174 </conditional>
5
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175 <param argument="--bisulfite" type="select" label="Bisulfite mapping">
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176 <option value="0">No bisulfite mapping</option>
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177 <option value="1">bisulfite mapping with methylC-seq/Lister et al.</option>
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178 <option value="2">bs-seq/Cokus et al. protocol</option>
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179 </param>
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180 <param argument="--minsize" type="integer" value="12" min="1" label="Minimum size of queries" />
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181 <param argument="--maxout" type="integer" min="0" value="0" optional="True"
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182 label="Maximum number of alignments that will be reported"/>
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183 <param argument="--accuracy" type="integer" value="85" min="1" max="100" label="Min percentage of matches per read in semi-global alignment" />
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184 <param argument="--hitstrategy" type="select" label="Hits to report?">
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185 <option value="1">report only best scoring hits</option>
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186 <option value="0">report all scoring hits</option>
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187 </param>
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188 <param argument="--prime5" type="text" label="add 5' adapter" help="default: none" />
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189 <param argument="--prime3" type="text" label="add 3' adapter" help="default: none"/>
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190 <param argument="--clipacc" value="70" type="integer" label="clipping accuracy" />
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191 <param argument="--polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" />
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192 <param argument="--autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter"/>
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193 <param argument="--hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping"/>
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194 <param argument="--order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" />
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195 <param argument="--differences" type="integer" min="0" value="1" label="search seeds initially with n differences"/>
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196 <param argument="--jump" type="integer" value="0" min="0" label="search seeds with jump size" help="(0=automatic) (default:0)?"/>
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197 <param argument="--evalue" type="float" min="0" value="5.000000" label="max evalue"/>
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198 <param argument="--maxinterval" type="integer" min="1" value="100" label="maximum width of a suffix array interval, i.e. a query seed will be omitted if it matches more than n times"/>
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199 <param argument="--nomatchfilename" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output unmatched reads"/>
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200 </inputs>
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201 <outputs>
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202 <data format="sam" name="segemehl_out" label="${tool.name} on ${on_string}"/>
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203 <data format="fastq" name="segemehl_outunmatched" label="${tool.name} unaligned reads ${on_string}">
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204 <filter>output_unmatched</filter>
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205 </data>
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206 </outputs>
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207 <tests>
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208 <test>
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209 <param name="genomeSource" value="history" />
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210 <param name="own_reference_genome" value="chr1.fa" />
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211 <param name="library" value="single" />
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212 <param name="input_query" value="test.fastq" />
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213 <param name="splits" value="nosplit" />
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214 <output name="segemehl_out" file="testmap.sam" lines_diff="2" />
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215 </test>
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216 <test>
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217 <param name="genomeSource" value="history" />
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218 <param name="own_reference_genome" value="chr1.fa" />
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219 <param name="library" value="single" />
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220 <param name="input_query" value="test.fastq" />
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221 <param name="splits" value="splits" />
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222 <param name="minsplicecover" value="40" />
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223 <param name="nomatchfilename" value="yes" />
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224 <output name="segemehl_out" file="testmap2.sam" lines_diff="2" />
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225 <output name="segemehl_outunmatched" file="testmap2.fastq" />
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226 </test>
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227 </tests>
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228 <help>
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229 <![CDATA[
0
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230
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231 .. class:: infomark
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232
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233 **What it does**
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234
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235 Segemehl_ is a short read mapper with gaps.
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236
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237 Segemehl_ is a software to map short sequencer reads to reference genomes.
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238 Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions.
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239 Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly.
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240 segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping.
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241
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242 .. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/
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243
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244
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245 ]]>
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246 </help>
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247 <citations>
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248 <citation type="doi">10.1371/journal.pcbi.1000502</citation>
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249 </citations>
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250 </tool>