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1 <tool id="ctat_fusion_inspector" name="ctat_fusion_inspector" version="1.0.0" profile="17.05">
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2 <description>In silico Validation of Fusion Transcript Predictions</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.0">fusion-inspector</requirement>
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5 </requirements>
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6 <command detect_errors="default">
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7 <![CDATA[
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8 FusionInspector
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9 --fusions $fusion_candidates_list
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10 --genome_lib "${genome_resource_lib.fields.path}"
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11 --left_fq $left_input
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12 --right $right_input
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13 --out_dir "subdir"
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14 --out_prefix "finspector"
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15 --prep_for_IGV
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16 #if $trinity_status.trinity=="true"
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17 --include_Trinity
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18 #end if
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19 ]]>
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20 </command>
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21 <stdio>
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22 <exit_code range="1:" level="fatal" description="Error returned from pipeline" />
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23 </stdio>
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24 <regex match="Must investigate error above."
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25 source="stderr"
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26 level="fatal"
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27 description="Unknown error encountered" />
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28 <inputs>
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29 <param format="tabular" name="fusion_candidates_list" type="data" multiple="True" label="Choose candidate list:" help="Fusion predictions"/>
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30 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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31 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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32 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR.
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33 <param name="method" type="select" label="Choose method:">
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34 <option value="HISAT">HISAT</option>
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35 <option value="STAR">STAR</option>
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36 <option value="GSNAP">GSNAP</option>
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37 </param>
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38 -->
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39 <conditional name="trinity_status">
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40 <param name="trinity" type="select" label="Use Trinity:">
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41 <option value="true">True</option>
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42 <option value="false">False</option>
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43 </param>
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44 </conditional>
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45 <param name="genome_resource_lib" type="select" label="Select a reference genome">
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46 <options from_data_table="ctat_genome_resource_libs">
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47 <filter type="sort_by" column="2" />
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48 <validator type="no_options" message="No indexes are available" />
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49 </options>
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50 </param>
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51 </inputs>
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52 <outputs>
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53 <data format="txt" name="finspector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/>
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54 <data format="txt" name="cytoBand" label="cytoBand" from_work_dir="subdir/cytoBand.txt"/>
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55 <data format="fasta" name="finspector_fa" label="finspector_fasta" from_work_dir="subdir/finspector.fa"/>
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56 <data format="bed" name="finspector_bed" label="finspector_bed" from_work_dir="subdir/finspector.bed"/>
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57 <data format="tabular" name="FusionJuncSpan" label="FusionJuncSpan" from_work_dir="subdir/finspector.igv.FusionJuncSpan"/>
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58 <data format="bed" name="junction_bed" label="junction_bed" from_work_dir="subdir/finspector.junction_reads.bam.bed"/>
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59 <data format="bam" name="junction_bam" label="junction_bam" from_work_dir="subdir/finspector.junction_reads.bam"/>
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60 <data format="bam" name="spanning_bam" label="spanning_bam" from_work_dir="subdir/finspector.spanning_reads.bam"/>
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61 <data format="bed" name="spanning_bed" label="spanning_bed" from_work_dir="subdir/finspector.spanning_reads.bam.bed"/>
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62 <data format="bed" name="trinity_bed" label="trinity_bed" from_work_dir="subdir/finspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed">
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63 <filter>trinity_status['trinity'] == "true"</filter>
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64 </data>
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65 <data format="txt" name="fusionPredictions" label="fusion_predictions.final" from_work_dir="subdir/finspector.fusion_predictions.final"/>
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66 <data format="txt" name="fusionPredictionsAbridged" label="fusion_predictions_abridged" from_work_dir="subdir/finspector.fusion_predictions.final.abridged"/>
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67 <data format="json" name="fusion_json" label="fusion_json" from_work_dir="subdir/finspector.fusion_inspector_web.json"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="fusion_candidates_list" value="FusionInspector/fusion_targets.A.txt,FusionInspector/fusion_targets.B.txt,FusionInspector/fusion_targets.C.txt" />
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72 <param name="left_input" value="FusionInspector/test.reads_1.fastq.gz" />
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73 <param name="right_input" value="FusionInspector/test.reads_2.fastq.gz" />
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74 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR.
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75 <param name="method" value="STAR" />
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76 -->
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77 <param name="trinity" value="false" />
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78 <!-- FIX - now that we added the CTAT resource lib path as a parameter, how do we find it for testing?
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79 <param name="genome_resource_lib.fields.path" value="?????" />
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80 -->
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81 <output name="finspector_idx" file="FusionInspector/test.reads_1_2.fa.fai" />
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82 <output name="cytoBand" file="FusionInspector/test.reads_1_2.cytoBand.tail.txt" compare="contains" />
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83 <output name="finspector_fa" file="FusionInspector/test.reads_1_2.fa" />
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84 <output name="finspector_bed" file="FusionInspector/test.reads_1_2.bed.sorted" sort="true" />
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85 <output name="FusionJuncSpan" >
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86 <assert_contents>
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87 <has_line_matching expression=".+" />
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88 <has_line line="#scaffold	fusion_break_name	break_left	break_right	num_junction_reads	num_spanning_frags	spanning_frag_coords" />
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89 </assert_contents>
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90 </output>
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91 <!-- sorted output sometimes matches, but simetimes not, so now I just test for similar size. -->
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92 <output name="junction_bed" file="FusionInspector/test.reads_1_2.junction_reads.bam.bed.sorted" sort="true" compare="sim_size" >
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93 <assert_contents>
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94 <has_line_matching expression=".+" />
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95 <has_n_columns n="12" />
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96 </assert_contents>
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97 </output>
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98 <output name="junction_bam" >
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99 <assert_contents>
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100 <has_line_matching expression=".+" />
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101 <!-- The following checks for the magic number at the start of the bam file -->
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102 <has_text_matching expression="\x1F\x8B" />
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103 </assert_contents>
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104 </output>
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105 <output name="spanning_bam" >
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106 <assert_contents>
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107 <has_line_matching expression=".+" />
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108 <!-- The following checks for the magic number at the start of the bam file -->
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109 <has_text_matching expression="\x1F\x8B" />
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110 </assert_contents>
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111 </output>
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112 <output name="spanning_bed" file="FusionInspector/test.reads_1_2.spanning_reads.bam.bed.sorted" sort="true" />
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113 <!--
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114 Since trinity is false in this test, trinity_bed does not exist.
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115 <output name="trinity_bed" />
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116 <assert_contents>
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117 <has_line_matching expression=".+" />
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118 </assert_contents>
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119 </output>
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120 -->
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121 <output name="fusionPredictions" >
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122 <assert_contents>
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123 <has_line_matching expression=".+" />
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124 <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags	Annotations	TrinityGG" />
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125 </assert_contents>
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126 </output>
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127 <output name="fusionPredictionsAbridged" >
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128 <assert_contents>
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129 <has_line_matching expression=".+" />
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130 <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	Annotations	TrinityGG" />
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131 </assert_contents>
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132 </output>
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133 <!-- So far in my testing of the fusion_json, I have had up to 18 different lines
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134 (9 positions values switched between two entries)- 64 gives some padding. -->
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135 <output name="fusion_json" file="FusionInspector/test.reads_1_2.web.json" lines_diff="64" />
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136
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137 </test>
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138 </tests>
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139 <help>
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140 .. class:: infomark
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141
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142 FusionInspector is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). FusionInspector assists in fusion transcript discovery by performing a supervised analysis of fusion predictions, attempting to recover and re-score evidence for such predictions. Please read more here_.
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143
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144 .. _here: https://github.com/FusionInspector/FusionInspector/wiki
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145
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146 **To Visualize Output**
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147
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148 After completion, results can be visualized in galaxy. Click on the output json file name in the history (on the right). A more detailed view of that file will be shown. Click on the button in the middle that looks like a bar chart. The visualization should now open for you to explore results.
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149
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150 **There are several output files for the CTAT Fusion Inspector Pipeline. Files of interest include:**
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151
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152 1. **fidx**: Finspector_fasta index file (required for visualization).
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153
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154 2. **cytoBand**: Cytogenetic information for hg19.
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155
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156 3. **finspector_fasta**: The candidate fusion-gene contigs.
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157
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158 4. **finspector_bed**: The reference gene structure annotations for fusion partners.
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159
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160 5. **FusionJuncSpan**: Tabular details on junction reads and spanning reads.
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161
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162 6. **junction_bed**: Alignments of the breakpoint-junction supporting reads.
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163
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164 7. **junction_bam**: Alignments of the breakpoint-junction supporting reads.
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165
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166 8. **spanning_bam**: Alignments of the breakpoint-spanning paired-end reads.
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167
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168 9. **spanning_bed**: Alignments of the breakpoint-spanning paired-end reads.
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169
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170 10. **trinity_bed**: Fusion-guided Trinity assembly.
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171
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172 11. **fusion_predictions.final**: All fusion evidence described.
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173
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174 12. **fusion_predictions_abridged**: encompasses all information in fusion_predictions.final excluding the names of the reads.
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175
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176 13. **fusion_json**: A logistical file that enables the visualization.
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177
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178 </help>
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179 <cite>
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180 </cite>
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181 </tool>
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