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comparison defuse.xml @ 6:6e30713cefb0 draft

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author Jim Johnson <jj@umn.edu>
date Mon, 07 Jan 2013 14:49:50 -0600
parents 3bd1087db05e
children 1ea6445491d4
comparison
equal deleted inserted replaced
5:3bd1087db05e 6:6e30713cefb0
69 </when> 69 </when>
70 <when value="history"> 70 <when value="history">
71 <param name="config" type="data" format="txt" label="Defuse Config file" help=""/> 71 <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
72 </when> <!-- history --> 72 </when> <!-- history -->
73 </conditional> <!-- refGenomeSource --> 73 </conditional> <!-- refGenomeSource -->
74 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"/> 74 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"
75 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run,
76 but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
75 <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> 77 <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
76 </inputs> 78 </inputs>
79 <outputs>
80 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
81 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
82 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">
83 <filter>keep_output == True</filter>
84 </data>
85 <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" />
86 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
87 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
88 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
89 <filter>do_get_reads == True</filter>
90 </data>
91 </outputs>
77 <configfiles> 92 <configfiles>
78 <configfile name="defuse_config"> 93 <configfile name="defuse_config">
79 #import ast 94 #import ast
80 #if $refGenomeSource.genomeSource == "history": 95 #if $refGenomeSource.genomeSource == "history":
81 #include raw $refGenomeSource.config.__str__ 96 #include raw $refGenomeSource.config.__str__
582 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path 597 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path
583 fi 598 fi
584 #end if 599 #end if
585 </configfile> 600 </configfile>
586 </configfiles> 601 </configfiles>
587 <outputs> 602
588 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
589 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
590 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output">
591 <filter>keep_output == True</filter>
592 </data>
593 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
594 <filter>do_get_reads == True</filter>
595 </data>
596 <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" />
597 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
598 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
599 </outputs>
600 <tests> 603 <tests>
601 </tests> 604 </tests>
602 <help> 605 <help>
603 **DeFuse** 606 **DeFuse**
604 607