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comparison defuse.xml @ 28:f51a95bdc38e

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Add breakpoints.bam output derived from breakpoints.genome.psl
author Jim Johnson <jj@umn.edu>
date Tue, 03 Sep 2013 06:41:19 -0500
parents d57fcac025e2
children 3e3ebdecb0e1
comparison
equal deleted inserted replaced
27:d57fcac025e2 28:f51a95bdc38e
73 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/> 73 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
74 --> 74 -->
75 <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" /> 75 <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" />
76 </when> <!-- full --> 76 </when> <!-- full -->
77 </conditional> <!-- defuse_param --> 77 </conditional> <!-- defuse_param -->
78 <param name="breakpoints_bam" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
78 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 79 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"
79 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 80 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run,
80 but they require considerable diskspace, and should be deleted and purged when no longer needed."/> 81 but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
81 <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> 82 <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
82 </inputs> 83 </inputs>
91 </data> 92 </data>
92 <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" /> 93 <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
93 <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" /> 94 <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
94 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads"> 95 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
95 <filter>do_get_reads == True</filter> 96 <filter>do_get_reads == True</filter>
97 </data>
98 <data format="bam" name="fusions_bam" label="${tool.name} on ${on_string}: fusions.bam">
99 <filter>breakpoints_bam == True</filter>
96 </data> 100 </data>
97 <!-- 101 <!--
98 expression_plot 102 expression_plot
99 circos plot 103 circos plot
100 --> 104 -->
580 ## copy primary results to output datasets 584 ## copy primary results to output datasets
581 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi 585 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
582 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi 586 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
583 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi 587 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
584 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi 588 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi
589 #if $breakpoints_bam:
590 if [ -e output_dir/results.filtered.tsv ] ${amp}${amp} [ -e output_dir/breakpoints.genome.psl ]
591 then
592 awk "\\$10 ~ /^(`awk '\\$1 ~ /[0-9]+/{print \\$1}' output_dir/results.filtered.tsv | tr '\n' '|'`)\\$/{print \\$0}" output_dir/breakpoints.genome.psl > breakpoints.genome.filtered.psl ${amp}${amp}
593 psl2sam.pl breakpoints.genome.filtered.psl > breakpoints.genome.filtered.sam ${amp}${amp}
594 samtools view -b -T /panfs/roc/rissdb/galaxy/genomes/NCBIM37/defuse/defuse.reference.fa -o breakpoints.genome.filtered.bam breakpoints.genome.filtered.sam ${amp}${amp}
595 samtools sort breakpoints.genome.filtered.bam breakpoints ${amp}${amp}
596 ## samtools index breakpoints.bam
597 cp breakpoints.bam $fusions_bam
598 fi
599 #end if
585 ## create html with links for output_dir 600 ## create html with links for output_dir
586 #if $defuse_out.__str__ != 'None': 601 #if $defuse_out.__str__ != 'None':
587 if [ -e $defuse_out ] 602 if [ -e $defuse_out ]
588 then 603 then
589 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out 604 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out