blast_contamination_search.all_mids.config 2.46 KB
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[interface]
classification = sequencing

[parameters]
; blast parameters
$;EXPECT$; = 1e-5
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$;FILTER$; = F
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$;DATABASE_MATCHES$; = 150
$;DESCRIPTIONS$; = 150
$;OTHER_OPTS$; =
; min identity percent to consider the hit as contamination 
$;PCI$; = 95
; min hit length percent to consider it as contamination
$;PCQ$; = 95
; The analyse name to display in ng6
$;ANALYSE_NAME$; = ContaminationSearch
; The analyse description to display in ng6
$;ANALYSE_DESCRIPTION$; = Recherche de contaminants par mids.
; The results archive name to display in ng6
$;RESULTS_ARCHIVE_NAME$; = `cat $;REPOSITORY_ROOT$;/output_repository/config_run/$;PIPELINEID$;_raw_input/run.raw.list | perl -lne "printf qq(basename %s .sff\n),\\$_;" | sh`_contamination.tar.gz

[input]
$;INPUT_FILE_LIST$;=$;REPOSITORY_ROOT$;/output_repository/sff_extract/$;PIPELINEID$;_all_mids/sff_extract.fasta.list
$;INPUT_FILE$;=
$;INPUT_DIRECTORY$;=
;; the following is only used when iterating over an INPUT_DIRECTORY
$;INPUT_EXTENSION$;=fna
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; the list of path to the formated database separated by a coma (database shouldnt have a "." in there name)
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$;DATABASES$; = ecoli536,genbank_phage,Saccharomyces_cerevisiae
; The run config file the analyse belongs to
$;NG6CFG_FILE$; = $;REPOSITORY_ROOT$;/output_repository/config_run/$;PIPELINEID$;_raw_input/run.cfg
; OR The project id the analyse belongs to
$;PROJECT_ID$; = 

[output]
$;OUTPUT_TOKEN$;=all_mids
$;OUTPUT_DIRECTORY$;=$;REPOSITORY_ROOT$;/output_repository/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
$;OUTPUT_M8_LIST$;= $;OUTPUT_DIRECTORY$;/$;COMPONENT_NAME$;.m8.list
$;OUTPUT_NAMES_LIST$;= $;OUTPUT_DIRECTORY$;/$;COMPONENT_NAME$;.names.list

[component]
$;COMPONENT_NAME$;=blast_contamination_search
$;DESCRIPTION$;=This script execute blast and filter it.  
$;WORKFLOW_REPOSITORY$;=$;REPOSITORY_ROOT$;/workflow/runtime/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
$;PIPELINE_TOKEN$;=unnamed

;The version,revision,tag here is set by an interpolated CVS tag
$;VERSION$;=$Name$
$;RELEASE_TAG$;=$Name$
$;REVISION$;=$Revision: 5503 $

$;TEMPLATE_XML$;=$;DOCS_DIR$;/$;COMPONENT_NAME$;.xml
$;ITERATOR1$;=i1
$;ITERATOR1_XML$;=$;DOCS_DIR$;/$;COMPONENT_NAME$;.$;ITERATOR1$;.xml
$;ITERATOR2$; = i2
$;ITERATOR2_XML$; = $;DOCS_DIR$;/$;COMPONENT_NAME$;.$;ITERATOR2$;.xml

;Distributed options
$;GROUP_COUNT$;=150
$;NODISTRIB$;=0

;the following keys are replaced at runtime by the invocation script
$;COMPONENT_CONFIG$;=
$;COMPONENT_XML$;=
$;PIPELINE_XML$;=
$;PIPELINEID$;=

[include]
$;PROJECT_CONFIG$;=