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1 <tool id="rna_star" name="RNA-STAR" version="0.2">
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2 <description>Gapped-read mapper for RNA-seq data</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.0e">rnastar</requirement>
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5 <requirement type="package">samtools</requirement>
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6 </requirements>
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7 <command>
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8 ##
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9 ## Run STAR.
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10 ##
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11
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12 STAR
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13 ## Can adjust this as appropriate for the system.
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14 --genomeLoad NoSharedMemory
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15
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16 --genomeDir ${refGenomeSource.index.fields.path}
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17 --readFilesIn $input1
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18 #if $singlePaired.sPaired == "paired"
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19 $singlePaired.input2
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20 #end if
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21
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22 --runThreadN 4
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23
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24 ## Parameters.
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25 #if $params.settingsType == "full":
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26 --chimSegmentMin $params.chim_segment_min
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27 --chimScoreMin $params.chim_score_min
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28 #end if
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29
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30 ## Needed to generate SAM tags for Cufflinks tools.
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31 --outSAMstrandField intronMotif
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32
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33 ;
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34
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35 ##
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36 ## BAM conversion.
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37 ##
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38
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39 ## Convert aligned reads.
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40 samtools view -Shb Aligned.out.sam | samtools sort - Aligned.out
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41
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42 ## Convert chimeric reads.
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43 #if $params.settingsType == "full" and $params.chim_segment_min > 0:
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44 ; samtools view -Shb Chimeric.out.sam | samtools sort - Chimeric.out
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45 #end if
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46 </command>
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47
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48 <stdio>
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49 <regex match=".*" source="both" level="warning" description="generic stdout/err chatter"/>
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50 </stdio>
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51
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52 <inputs>
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53 <param name="jobName" type="text" size="120" value="rna-star run" label="Job narrative (added to output names)"
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54 help="Only letters, numbers and underscores (_) will be retained in this field">
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55 <sanitizer invalid_char="">
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56 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
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57 </sanitizer>
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58 </param>
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59 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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60 <conditional name="singlePaired">
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61 <param name="sPaired" type="select" label="Single ended or mate-pair ended reads in this library?">
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62 <option value="single" selected="true">Single-end</option>
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63 <option value="paired">Paired-end</option>
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64 </param>
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65 <when value="single">
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66 <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
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67 </when>
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68 <when value="paired">
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69 <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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70 <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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71 </when>
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72 </conditional>
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73
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74 <!-- Genome source. -->
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75 <conditional name="refGenomeSource">
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76 <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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77 <option value="indexed">Use a built-in index</option>
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78 <option value="history">Use one from the history</option>
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79 </param>
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80 <when value="indexed">
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81 <param name="index" type="select" label="Select a reference genome">
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82 <options from_data_table="rnastar_indexes">
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83 <filter type="sort_by" column="2"/>
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84 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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85 </options>
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86 </param>
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87 </when>
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88 <when value="history">
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89 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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90 </when>
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91 </conditional>
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92
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93 <!-- Parameter settings. -->
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94 <conditional name="params">
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95 <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR parameter.">
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96 <option value="preSet" selected="true">Use Defaults</option>
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97 <option value="full">Full parameter list</option>
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98 </param>
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99 <when value="preSet" />
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100 <!-- Full/advanced params. -->
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101 <when value="full">
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102 <param name="chim_segment_min" type="integer" min="0" value="0" label="Minimum chimeric segment length" />
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103 <param name="chim_score_min" type="integer" min="0" value="0" label="Minimum total (summed) score of the chimeric segments" />
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104 </when>
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105 </conditional>
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106 </inputs>
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107
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108 <outputs>
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5
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109 <data format="txt" name="output_log" label="${on_string}_${jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction">
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4
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110 <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
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111 <actions>
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112 <conditional name="refGenomeSource.genomeSource">
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113 <when value="indexed">
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114 <action type="metadata" name="dbkey">
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115 <option type="from_data_table" name="star_indexes" column="1" offset="0">
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116 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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117 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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118 </option>
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119 </action>
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120 </when>
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121 <when value="history">
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122 <action type="metadata" name="dbkey">
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123 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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124 </action>
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125 </when>
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126 </conditional>
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127 </actions>
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128 </data>
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5
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129 <data format="bam" name="chimeric_reads" label="${on_string}_${jobName}_starmappedchim.bam"
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130 from_work_dir="Chimeric.out.bam">
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131 <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
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132 <actions>
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133 <conditional name="refGenomeSource.genomeSource">
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134 <when value="indexed">
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135 <action type="metadata" name="dbkey">
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136 <option type="from_data_table" name="star_indexes" column="1" offset="0">
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137 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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138 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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139 </option>
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140 </action>
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141 </when>
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142 <when value="history">
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143 <action type="metadata" name="dbkey">
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144 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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145 </action>
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146 </when>
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147 </conditional>
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148 </actions>
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149 </data>
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5
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150 <data format="interval" name="splice_junctions" label="${on_string}_${jobName}_starsplicejunct.bed"
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151 from_work_dir="SJ.out.tab">
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152 <actions>
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153 <conditional name="refGenomeSource.genomeSource">
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154 <when value="indexed">
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155 <action type="metadata" name="dbkey">
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156 <option type="from_data_table" name="star_indexes" column="1" offset="0">
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157 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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158 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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159 </option>
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160 </action>
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161 </when>
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162 <when value="history">
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163 <action type="metadata" name="dbkey">
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164 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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165 </action>
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166 </when>
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167 </conditional>
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168 </actions>
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169 </data>
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5
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170 <data format="bam" name="mapped_reads" label="${on_string}_${jobName}_starmapped.bam"
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171 from_work_dir="Aligned.out.bam">
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172 <actions>
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173 <conditional name="refGenomeSource.genomeSource">
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174 <when value="indexed">
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175 <action type="metadata" name="dbkey">
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176 <option type="from_data_table" name="star_indexes" column="1" offset="0">
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177 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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178 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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179 </option>
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180 </action>
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181 </when>
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182 <when value="history">
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183 <action type="metadata" name="dbkey">
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184 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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185 </action>
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186 </when>
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187 </conditional>
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188 </actions>
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189 </data>
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190 </outputs>
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191 <help>
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192
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193 **Attributions**
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194
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195 Note that each component has its own license. Good luck with figuring out your obligations.
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196
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197 rna_star - see the web site at rna_star_
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198
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199 For details, please see the rna_starMS_
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200 "STAR: ultrafast universal RNA-seq aligner"
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201 A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
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202
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203 Galaxy_ (that's what you are using right now!) for gluing everything together
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204
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205 Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
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206
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207 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
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208 and odds and ends of other code and documentation comprising this tool was
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209 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
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210
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211 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
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212 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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213 .. _rna_star: http://code.google.com/p/rna-star/
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214 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
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215 .. _Galaxy: http://getgalaxy.org
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216
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217 </help>
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218 </tool>
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