-
-" > "$HTML_REPORT"
-
-
-MARINE
-
diff -r e6e516ff34a8 -r dbb83adec9eb crac/crac-index.xml
--- a/crac/crac-index.xml Fri Sep 13 09:51:59 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-
-
- Create genome indexes available to be used with CRAC mapping/annotation tool
-
-
- crac-index-wrapper.sh "$output_name" "$output" "$output.files_path" "$bucket" "$input_file"
-
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-**What it does**
-
-Crac-index generates an indexed genome from a fasta file. This is especially useful for the Crac mapping/annotation tool.
-
-----------------------
-
-**Input Formats**
-
-Crac-index takes as input files any fasta or multi-fasta files.
-
-----------------------
-
-**Outputs**
-
-Crac-index on Galaxy produces a composite output named crac-index, which is made of a ssa file and a conf file. Both are required to the use of your index.
-
-----------------------
-
-**Crac-index settings**
-
-
-Usage : ./crac-index [options] command output_file input_file
-
- command must be :
- index: create an index on the specified input file(s).
-
- options can be :
-
- -b bucket_size the size of the bucket for the index construction
- (default 100000000)
- -d diff-cover parameter for the index construction (default 1024)
- -v verbose mode
-
- Examples:
- ./crac-index index myIndex sequence1.fa sequence2.fa sequence3.fa
- You can specify FASTA or MultiFASTA file(s).
- In this example, two files will be created:
- - myIndex.ssa (index storing the compressed sequences)
- - myIndex.conf (information on sequence names and length)
-
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diff -r e6e516ff34a8 -r dbb83adec9eb crac/crac.xml
--- a/crac/crac.xml Fri Sep 13 09:51:59 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,265 +0,0 @@
-
-
-
- crac
-
- Analyzing RNAs in high-throughput sequencing data
- crac_wrapper.sh
- #if $Genome.which_genome == "prebuilt"
- "$Genome.prebuilt_genome.fields.path"
- #else
- "$Genome.index_input.extra_files_path"
- #end if
- #if $condi_compressed == "yes"
- --gz
- #end if
- $output_name.extra_files_path
- -r $input -k $kmer_length --read-length $read_length --sam $output_name
- #if $condi_deep_snp.deepSNP == "yes"
- --deep-snv --nb-nucleotides-snv-comparison $condi_deep_snp.nb_nucleotides_snp_comparison
- #end if
- #if $choixSettings.settings == "experimental"
- --max-splice-length $choixSettings.max_splice_length
- --max-bio-indel $choixSettings.max_bio_indel
- --min-duplication $choixSettings.min_duplication
- --max-duplication $choixSettings.max_duplication
- --min-percent-single-loc $choixSettings.min_percent_single_loc
- --min-percent-duplication-loc $choixSettings.min_percent_duplication_loc
- --max-bases-randomly-matched $choixSettings.max_bases_randomly_matched
- --max-extension-length $choixSettings.max_extension_length
- --min-support-no-cover $choixSettings.min_support_no_cover
- --min-break-length $choixSettings.min_break_length
- #end if
- #if str($detailed_sam) == "yes"
- --detailed-sam
- #end if
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- k-mer length must be carefully chosen. A k-mer of that length must map to a unique location in the genome with a high probability. Recommended value for the human genome: 22
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-**What it does**
-
-CRAC proposes a novel way of analyzing reads that integrates genomic locations
-and local coverage, and delivers all above mentioned predictions in a single
-step. CRAC uses a double k-mer profiling approach to detect candidate
-mutations, indels, splice or fusion junctions in each single read.
-
-.. _CRAC: http://crac.gforge.inria.fr/
-
-If you use this tool, please cite:
- - Philippe N., Salson M., Commes T., Rivals E., `"CRAC: an integrated approach to the analysis of RNA-seq reads"`__, Genome Biology (2013), 14:R30, doi: 10.1186/gb-2013-14-3-r30.
-
-.. __: http://genomebiology.com/2013/14/3/R30/
-
-------
-
-**Input formats**
-
-CRAC accepts files in FASTA, FASTQ or any text format (txt, raw, ...).
-
-------
-
-**Output**
-
-The output is in SAM format. If you choose the detailed SAM output, CRAC adds several flags to tell more informations. You can see the details here: http://crac.gforge.inria.fr/index.php?id=sam-documentation
-
-
-------
-
-**Crac settings**
-
-Main options are displayed at the top of the page. If you're an experimented user, you can choose to display
-the whole Crac setting. Most of the options in Crac have been implemented here.
-
-------
-crac 1.3.0 Compiled on Sep 13 2013.
-
- -h, --help print this help and exit
- -f, --full-help print a complete help and exit
- -v print version and exit
-
-Mandatory arguments
- -i set genome index file (without the extension filename)
- -r [FILE2] set read file. Specify FILE2 in case of paired-end reads
- -k set k-mer length
- -o, --sam set SAM output filename or print on STDOUT with "-o -" argument
-
-Optional arguments
- * Protocol
- --stranded set the read mapping with for a strand specific library (DEFAULT non-strand specific)
-
- * Efficiency
- --nb-threads set the number of worker threads (DEFAULT 1)
- --read-length, -m set read length in case of all reads have the same length to optimize
- CPU and memory times
- --treat-multiple consider alignments with multiple locations (>max-duplication) rather than considering a no-alignment in the SAM file
- --max-locs set the maximum number of locations on the reference index (DEFAULT 300)
-
- * Accuracy
- --no-ambiguity discard biological events (splice, snv, indel, chimera) which have several matches on the reference index
-
-
-Optional output arguments
- --all set output base filename for all causes following
- --gz all output files specified after this argument are gzipped
-
- * Summary and statistics
- --summary set output summary file
- * Mapping
- --single set output single file
- --duplicate set output duplication file
- --multiple set output multiple file
- --none set output none file
- --normal set output normal file
- --almost-normal set output almost normal file
-
- * Biological causes
- --snv set output SNV file
- --indel set output short indel file
- --splice set output splice junction file
- --weak-splice set output coverless splice junction file
- --chimera set output chimera junction file
- --paired-end-chimera set output for paired-end chimera file
- --biological set output bio-undetermined file
-
- * Sequence errors
- --errors set output sequence errors file
-
- * Repetition
- --repeat set output repetition file
-
- * Other causes
- --undetermined set output undetermined file
- --nothing set output nothing file
-
-Optional process for specific research
- --deep-snv will search hard to find SNPs
- --stringent-chimera will search chimeras with more accuracy (but less sensitivity)
-
-Optional process launcher (once must be selected)
- * Exact matching tool
- --emt launch CRAC-emt for exact mapping of short reads
-
- * Server tool (for debugging)
- --server launch CRAC server,the output arguments will
- not be taken into account
- --input-name-server DEFAULT classify.fifo
- --output-name-server DEFAULT classify.out.fifo
-
-Additional settings for users
- * Sam output file
- --detailed-sam more informations are added in SAM output file
-
- * Mapping
- --min-percent-single-loc DEFAULT 0.15
- --min-duplication DEFAULT 2
- --max-duplication DEFAULT 9
- --min-percent-duplication-loc DEFAULT 0.15
- --min-percent-multiple-loc DEFAULT 0.50
- --min-repetition DEFAULT 20
- --min-percent-repetition-loc DEFAULT 0.20
- * Biological causes
- --max-splice-length DEFAULT 300000
- --max-paired-end-length DEFAULT 300000
- --max-bio-indel DEFAULT 15
- --max-bases-retrieved DEFAULT 15
- * Undetermined
- --min-support-no-cover DEFAULT 1.30
-
-Additional settings for advanced users
- * Break verification and fusion (merging mirage breaks)
- --min-break-length DEFAULT 0.50
- --max-bases-randomly-matched DEFAULT 10
- --max-extension-length DEFAULT 10
-
- * Threading
- --nb-tags-info-stored DEFAULT 1000
-
- * Deep SNV search option
- --nb-nucleotides-snv-comparison DEFAULT 8
-
-
-
diff -r e6e516ff34a8 -r dbb83adec9eb crac/crac_wrapper.sh
--- a/crac/crac_wrapper.sh Fri Sep 13 09:51:59 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-#!/bin/sh
-
-# Recovering special parameters from crac.xml
-###############################################################
-CRAC_BINARY=crac
-INDEX_INPUT="$1"
-
-# Getting the indexed genome value
-###############################################################
-# Getting the indexed Genome name without the extension
-if [ -d "$INDEX_INPUT" ]; then # If $INDEX_INPUT is a directory (that is to say an index from the history)
- cpt=0
- for fichier in $INDEX_INPUT/*.ssa
- do
- if [ $((++cpt)) -gt 1 ]; then #More than 1 '.ssa' file is not expected
- echo "Warning:Multiple indexes found [$INDEX]" >&2
- fi
- INDEX=${fichier%%.ssa} #Getting the index from history
- done
- else
- INDEX="$INDEX_INPUT" #Getting the prebuilt index
-fi
-if [ ! -f "$INDEX.ssa" -a ! -f "$INDEX.conf" ]; then #Both '.ssa' and '.conf' files are required
- echo "Error:Index not found [$INDEX]" >&2
- exit 1
-fi
-
-# Execution of the command line (Submiting job to the cluster)
-###############################################################
-shift 2 #Avoiding index_input and output_name.extra_files_path
-
-CRAC_CMD_LINE=""$CRAC_BINARY" -i "$INDEX" "$@""
-
-out=`$CRAC_CMD_LINE`
-
-exit 0
-
diff -r e6e516ff34a8 -r dbb83adec9eb crac/tool_dependencies.xml
--- a/crac/tool_dependencies.xml Fri Sep 13 09:51:59 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-
-
-
-
-
- https://gforge.inria.fr/frs/download.php/32471/crac-1.3.0.tar.gz
- ./configure
- make
- make check
-
-
-
-CRAC requires g++ 4.3 or later.
-
-
-