Mercurial > repos > rnateam > segemehl

annotate segemehl.xml @ 7:be1a3cc2cf45 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit b193689f9f30ce65a77be2d2c00929e3335a7d82
author bgruening
date Wed, 26 Jul 2017 15:25:28 -0400
parents c6cef240817e
children 90b8941e5115
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1 <tool id="segemehl" name="segemehl" version="0.2.0.3">
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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"
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8 source="both"
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9 level="fatal"
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10 description="Execution halted." />
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11 </stdio>
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12 <command>
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13 <![CDATA[
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14 ## prepare segemehl index if no reference genome is supplied
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15 #if $refGenomeSource.genomeSource == "history":
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16 mkdir ./temp_index/ &&
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17 #set $temp_index = './temp_index/temp.idx'
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18 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome &&
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19 #else:
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20 #set $temp_index = $refGenomeSource.index.fields.index_path
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21 #end if
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22
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23 ## execute segemehl
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24 segemehl.x
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25
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26 ## number of threads
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27 -t "\${GALAXY_SLOTS:-12}"
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28
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29 #if $refGenomeSource.genomeSource == "history":
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30 -d $refGenomeSource.own_reference_genome
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31 #else:
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32 -d ${refGenomeSource.index.fields.db_path}
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33 #end if
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34
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35 -i $temp_index
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36
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37 ## check for single/pair-end
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38 #if str( $library.type ) == "single":
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39 #set $query_list = list()
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40 ## prepare inputs
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41 #for $fastq in $library.input_query:
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42 $query_list.append('%s' % $fastq )
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43 #end for
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44 -q "#echo ' '.join( $query_list )#"
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45 #else
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46 ## prepare inputs
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47 #set $mate1 = list()
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48 #set $mate2 = list()
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49 #for $mate_pair in $library.mate_list:
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50 $mate1.append( str($mate_pair.first_strand_query) )
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51 $mate2.append( str($mate_pair.second_strand_query) )
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52 #end for
5
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53
0
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54 -q #echo ','.join($mate1)
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55 -p #echo ','.join($mate2)
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56
0
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57 -I $library.maxinsertsize
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58 #end if
6
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59 -m $minsize
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60 -A $accuracy
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61 -H $hitstrategy
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62 #if str( $prime5 ).strip():
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63 -P "$prime5"
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64 #end if
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65 #if str( $prime3 ).strip():
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66 -Q "$prime3"
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67 #end if
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68 $polyA
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69 $autoclip
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70 $hardclip
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71 $order
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72 #if $maxout:
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73 --maxout $maxout
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74 #end if
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75 #if str( $splitreads.splits ) == "splits":
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76 --splits
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77 --minsplicecover $splitreads.minsplicecover
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78 --minfragscore $splitreads.minfragscore
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79 --minfraglen $splitreads.minfraglen
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80 --splicescorescale $splitreads.splicescorescale
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81 #end if
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82 -M $maxinterval
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83 -E $evalue
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84 -D $differences
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85 -s
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86 -o '$segemehl_out'
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87 ]]>
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88 </command>
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89 <inputs>
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90 <conditional name="refGenomeSource">
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91 <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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92 <option value="indexed">Use a built-in index</option>
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93 <option value="history">Use one from the history</option>
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94 </param>
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95 <when value="indexed">
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96 <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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97 <options from_data_table="segemehl_indexes">
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98 <column name="value" index="0"/>
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99 <column name="dbkey" index="1"/>
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100 <column name="name" index="2"/>
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101 <column name="db_path" index="3"/>
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102 <column name="index_path" index="4"/>
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103 <filter type="sort_by" column="2"/>
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104 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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105 </options>
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106 </param>
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107 </when> <!-- build-in -->
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108 <when value="history">
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109 <param name="own_reference_genome" type="data" format="fasta" label="Select the reference genome" />
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110 </when> <!-- history -->
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111 </conditional> <!-- refGenomeSource -->
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112
5
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113 <conditional name="library">
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114 <param name="type" type="select" label="Is this library paired-end?">
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115 <option value="single">Single-end</option>
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116 <option value="paired">Paired-end</option>
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117 </param>
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118 <when value="single">
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119 <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" />
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120 </when>
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121 <when value="paired">
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122 <!-- ToDo paired coolections -->
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123 <repeat name="mate_list" title="Paired End Pairs" min="1">
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124 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" />
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125 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" />
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126 </repeat>
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127 <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" />
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128 </when>
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129 </conditional>
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130
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131 <conditional name="splitreads">
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132 <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)">
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133 <option value="nosplit">No splits</option>
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134 <option value="splits">Split reads</option>
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135 </param>
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136 <when value="splits">
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137 <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" />
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138 <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" />
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139 <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" />
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140 <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score"
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141 help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" />
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142 <param name="sevalue" type="float" min="0" value="50.000000" label="max split evalue" help="(--maxsplitevalue)"/>
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143 </when>
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144 <when value="nosplit">
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145 </when>
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146 </conditional>
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147
5
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148 <param name="minsize" type="integer" value="12" min="1" label="Minimum size of queries" help="(-m)" />
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149 <param name="maxout" type="integer" min="0" value="0" optional="True"
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150 label="Maximum number of alignments that will be reported" help="(--maxout)" />
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151 <param name="accuracy" type="integer" value="85" min="1" max="100" label="Min percentage of matches per read in semi-global alignment" help="(-A)" />
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152 <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)">
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153 <option value="1">report only best scoring hits</option>
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154 <option value="0">report all scoring hits</option>
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155 </param>
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156 <param name="prime5" type="text" label="add 5' adapter" help="default: none (-Q)" />
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157 <param name="prime3" type="text" label="add 3' adapter" help="default: none (-P)"/>
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158 <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/>
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159 <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/>
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160 <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="(-C)"/>
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161 <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/>
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162 <param name="differences" type="integer" min="0" value="1" label="search seeds initially with n differences" help="(--differences)"/>
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163 <param name="evalue" type="float" min="0" value="5.000000" label="max evalue" help="(--evalue)"/>
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164 <param name="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" help="(--maxinterval)"/>
5
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165 </inputs>
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166 <outputs>
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167 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/>
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168 </outputs>
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169 <tests>
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170 <test>
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171 <param name="genomeSource" value="history" />
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172 <param name="own_reference_genome" value="chr1.fa" />
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173 <param name="library" value="single" />
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174 <param name="input_query" value="test.fastq" />
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175 <param name="splits" value="nosplit" />
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176 <output name="segemehl_out" file="testmap.sam" lines_diff="2" />
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177 </test>
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178 <test>
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179 <param name="genomeSource" value="history" />
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180 <param name="own_reference_genome" value="chr1.fa" />
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181 <param name="library" value="single" />
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182 <param name="input_query" value="test.fastq" />
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183 <param name="splits" value="splits" />
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184 <param name="minsplicecover" value="40" />
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185 <output name="segemehl_out" file="testmap2.sam" lines_diff="2" />
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186 </test>
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187 </tests>
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188 <help>
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189 <![CDATA[
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190
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191 .. class:: infomark
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192
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193 **What it does**
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194
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195 Segemehl_ is a short read mapper with gaps.
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196
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197 Segemehl_ is a software to map short sequencer reads to reference genomes.
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198 Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions.
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199 Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly.
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200 segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping.
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201
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202 .. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/
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203
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204
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205 ]]>
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206 </help>
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207 <citations>
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208 <citation type="doi">10.1371/journal.pcbi.1000502</citation>
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209 </citations>
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210 </tool>