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annotate star_fusion.xml @ 6:ac246b8ab8a5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 38b164ccb9b3cdfb58d83cdc1f05063a40123bab-dirty
author yhoogstrate
date Fri, 26 Aug 2016 04:47:48 -0400
parents c53938d8a6da
children
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1 <tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07">
0
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2 <description>detect fusion genes in RNA-Seq data</description>
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3 <requirements>
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4 <!-- Bio-conda -->
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5 <requirement type="package" version="0.5.4">star-fusion</requirement>
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6 </requirements>
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7
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8 <stdio>
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9 <regex match="command not found" source="stderr" level="fatal"/>
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10 <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>
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11 <regex match="FATAL ERROR" source="stderr" level="fatal"/>
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12
0
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13 <regex match="Warning:" source="stderr" level="warning"/>
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14 <regex match="CMD:" source="stderr" level="warning"/>
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16 <regex match="-done creating index file:" source="stderr" level="warning"/>
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17 <regex match="-parsing GTF file:" source="stderr" level="warning"/>
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18 <regex match="-building interval tree" source="stderr" level="warning"/>
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19 <regex match="-parsing fusion evidence:" source="stderr" level="warning"/>
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20 <regex match="-mapping reads to genes" source="stderr" level="warning"/>
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21 <regex match="-outputting fusion candidates to file:" source="stderr" level="warning"/>
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23 <regex match="Process complete" source="stderr" level="warning"/>
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24 </stdio>
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26 <version_command>STAR-Fusion --version 2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>
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27
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28 <command><![CDATA[
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29 ## 1. do blastn on the genome reference
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30 if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then
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31 gzip_suffix='' ;
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32 else
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33 ## Older versions of gzip do not support the -k option to keep
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34 ## the original file - this should be an universion solution
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35
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36 gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' &&
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37 gzip_suffix='.gz' ;
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38 fi &&
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39
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40 ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
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41 prep_genome_lib.pl
2
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42 --genome_fa '${fasta_type.ownFile}'
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43 --gtf '${geneModel}'
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44 --blast_pairs "${blast_pairs}\$gzip_suffix"
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45 --CPU \${GALAXY_SLOTS:-1}
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46 --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
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47 &&
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48
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49 ## 3. Run STAR-Fusion
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50 STAR-Fusion
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51
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52 #if str($input_params.input_source) == "use_chimeric":
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53 --chimeric_junction '${input_params.chimeric_junction}'
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54 #else:
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55 --left_fq '${input_params.left_fq}'
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56 #if $input_params.right_fq:
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57 --right_fq '${input_params.right_fq}'
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58 #end if
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59 #end if
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60
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61 --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
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62
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63 #if str($params.settingsType) == "full":
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64 --min_junction_reads $params.min_junction_reads
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65 --min_sum_frags $params.min_sum_frags
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66 --max_promiscuity $params.max_promiscuity
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67 --min_novel_junction_support $params.min_novel_junction_support
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68 --min_alt_pct_junction $params.min_alt_pct_junction
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69 --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
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70 --E $params.E
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71 #end if
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72 ]]></command>
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73
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74 <inputs>
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75 <conditional name="input_params">
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76 <param name="input_source"
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77 type="select"
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78 label="Use output from earlier STAR run or let STAR Fusion control running STAR">
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79 <option value="use_chimeric">Use output from earlier STAR</option>
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80 <option value="use_fastq">Let STAR Fusion control running STAR</option>
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81 </param>
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82 <when value="use_chimeric">
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83 <param name="chimeric_junction"
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84 type="data"
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85 format="interval"
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86 argument="--chimeric_junction"
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87 label="Chimeric junction file from STAR (with STAR-Fusion settings)"/>
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88 </when>
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89 <when value="use_fastq">
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90 <param name="left_fq"
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91 type="data"
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92 format="fastqsanger"
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93 argument="--left_fq"
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94 label="left.fq file"/>
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95 <param name="right_fq"
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96 type="data"
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97 format="fastqsanger"
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98 optional="true"
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99 argument="--right_fq"
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100 label="right.fq file (actually optional, but highly recommended)"/>
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101 </when>
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102 </conditional>
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103
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104 <!-- Genome source. -->
2
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105 <conditional name="fasta_type">
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106 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
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107 <option value="cached">Locally Cached sequences</option>
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108 <option value="history" selected="true">Sequences from your history</option>
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109 </param>
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110 <when value="cached">
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111 <param name="ownFile"
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112 type="select" label="Genome to search">
4
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113 <options from_data_table="all_fasta">
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114 <column name="value" index="3"/>
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115 <column name="dbkey" index="1"/>
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116 </options>
2
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117 </param>
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118 </when>
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119 <when value="history">
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120 <param name="ownFile"
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121 type="data"
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122 format="fasta"
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123 metadata_name="dbkey"
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124 label="Select the reference genome (FASTA file)"/>
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125 </when>
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126 </conditional>
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127
0
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128 <param name="geneModel"
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129 type="data"
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130 format="gff3,gtf"
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131 label="Gene model (gff3,gtf) file for splice junctions and fusion gene detection"/>
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132 <param name="blast_pairs"
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133 type="data"
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134 format="tabular"
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135 label="Result of BLAST+-blastn of the reference fasta sequence with itself"
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136 help="Run blastn with '-outputfmt 6' or choose 'Tabular (standard 12 columns)' in the Galaxy wrapper. For human data it is recommended to obtain it from here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/"/>
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137
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138 <conditional name="params">
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139 <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR Fusion parameter.">
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140 <option value="default" selected="true">Use Defaults</option>
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141 <option value="full">Full parameter list</option>
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142 </param>
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143 <when value="default" />
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144 <when value="full"><!-- Full/advanced params. -->
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145 <param name="min_junction_reads"
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146 type="integer" value="1"
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147 label="minimum number of junction-spanning reads required."
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148 argument="--min_junction_reads"/>
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149 <param name="min_sum_frags"
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150 type="integer"
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151 value="2"
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152 label="minimum fusion support = (#junction_reads + #spanning_frags)"
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153 argument="--min_sum_frags"/>
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154 <param name="max_promiscuity"
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155 type="integer"
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156 value="3"
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157 label="maximum number of partners allowed for a given fusion"
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158 argument="--max_promiscuity"/>
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159 <param name="min_novel_junction_support"
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160 type="integer"
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161 value="3"
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162 label="minimum of 3 junction reads required if breakpoint lacks involvement of only reference junctions"
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163 argument="--min_novel_junction_support"/>
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164 <param name="min_alt_pct_junction"
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165 type="float"
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166 value="10"
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167 label="10% of the dominant isoform junction support"
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168 argument="--min_alt_pct_junction"/>
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169 <param name="aggregate_novel_junction_dist"
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170 type="integer"
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171 value="5"
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172 label="non-ref junctions within 5 are merged into single calls"
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173 argument="--aggregate_novel_junction_dist"/>
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174 <param name="E"
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175 type="float"
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176 value="0.001"
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177 label="E-value threshold for blast searches"
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178 argument="-E"/>
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179 </when>
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180 </conditional>
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181 </inputs>
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182
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183 <outputs>
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184 <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_candidates.final" from_work_dir="star-fusion.fusion_candidates.final"/>
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185 </outputs>
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186
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187 <tests>
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188 <test>
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189 <param name="input_source" value="use_chimeric" />
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190 <param name="chimeric_junction" ftype="interval" value="test1.tabular" />
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191 <param name="fasta_type_selector" value="history" />
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192 <param name="ownFile" ftype="fasta" value="test1.fa" />
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193 <param name="geneModel" ftype="gtf" value="test1.gtf" />
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194 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
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195 <param name="settingsType" value="default" />
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196
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197 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
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198 <output name="output_final">
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199 <assert_contents>
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200 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
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201 <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
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202 </assert_contents>
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203 </output>
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204 </test>
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205 <test>
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206 <param name="input_source" value="use_fastq" />
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207 <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/>
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208 <param name="fasta_type_selector" value="history" />
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209 <param name="ownFile" ftype="fasta" value="test1.fa" />
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210 <param name="geneModel" ftype="gtf" value="test1.gtf" />
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211 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
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212 <param name="settingsType" value="default" />
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213
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214 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
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215 <output name="output_final">
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216 <assert_contents>
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217 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
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218 <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
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219 </assert_contents>
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220 </output>
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221 </test>
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222 </tests>
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223 <help>
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224 **What it does**
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225
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226 STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
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227
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228 **Input**
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229
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230 A reference genome and corresponding protein-coding gene annotation set, including blast-matching gene pairs must be provided to STAR-Fusion.
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231
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232 We provide several alternative resources for human fusion transcript detection depending on whether you want to use GRCh37 or GRCh38 reference human genomes and corresponding Gencode annotation sets. Options are available here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/, so choose one. The gene annotations in each case are restricted to the protein-coding and lincRNA transcripts.
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233
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234 In Galaxy you can create such files with the *ncbi_blast_plus* tool suite containing *blastn*: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
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235
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236 More info: https://github.com/STAR-Fusion/STAR-Fusion/wiki
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237
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238 </help>
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239
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240 <citations>
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241 <citation type="bibtex">
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242 @unpublished{star_fusion,
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243 author = {Brian Haas and Nicolas Stransky and Daniel Nicorici},
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244 title = {STAR-Fusion},
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245 url = {https://github.com/STAR-Fusion/STAR-Fusion}
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246 }
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247 </citation>
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248 </citations>
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249 </tool>