Mercurial > repos > malbuquerque > factera
comparison factera/factera.xml @ 30:12c14221b302 draft default tip
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author | malbuquerque |
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date | Fri, 16 Jan 2015 20:15:33 -0500 |
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29:b54954734c9f | 30:12c14221b302 |
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1 <tool id="factera" name="FACTERA" version="1.4.3"> | |
2 | |
3 <description>Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm</description> | |
4 | |
5 <requirements> | |
6 <requirement type="package" version="0.1.19">samtools</requirement> | |
7 <requirement type="package" version="2.2.26+">blast+</requirement> | |
8 <requirement type="package" version="310">ucsc_user_apps</requirement> | |
9 <requirement type="package" version="5.18.1">perl</requirement> | |
10 <requirement type="package" version="1.4.3">factera</requirement> | |
11 <requirement type="package" version="3.0608">perl_descriptive_statistics</requirement> | |
12 <requirement type="set_environment">FACTERA_DIR</requirement> | |
13 </requirements> | |
14 | |
15 <command> | |
16 <!-- Run commands using Galaxy perl --> | |
17 | |
18 ln -s $sortedBam ./input.bam; | |
19 ln -s $sortedBam.metadata.bam_index ./input.bam.bai; | |
20 | |
21 | |
22 #if $cond.additionalOpt == "no" | |
23 perl \$FACTERA_DIR/factera-v1.4.3.pl -F -o ./ input.bam $exonBed $genome2Bit; | |
24 #else | |
25 perl \$FACTERA_DIR/factera-v1.4.3.pl -F -r $cond.r -m $cond.m -x $cond.x -s $cond.s -f $cond.f -S $cond.S | |
26 -k $cond.k -c $cond.c -b $cond.b -p $cond.p -a $cond.a -o ./ input.bam $exonBed $genome2Bit; | |
27 #end if | |
28 | |
29 <!-- Keep only the fusion file --> | |
30 if [ -e *fusions.txt ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi | |
31 </command> | |
32 | |
33 <inputs> | |
34 <param format="bam" name="sortedBam" type="data" label="Alignment in BAM format" /> | |
35 <param format="bed" name="exonBed" type="data" label="Genomic coordinates with gene/exon names in fourth column" /> | |
36 <param format="twobit" name="genome2Bit" type="data" label="Two bit reference sequence" /> | |
37 <conditional name="cond"> | |
38 <param type="select" name="additionalOpt" label="Additional Options"> | |
39 <option value="yes">Yes</option> | |
40 <option value="no" selected="True">No</option> | |
41 </param> | |
42 <when value="yes"> | |
43 <!-- Names follow command line flags in factera.pl --> | |
44 <param type="integer" name="r" label="Minimum number of breakpoint-scanning reads required for output" value="5"/> | |
45 <param type="integer" name="m" label="Minimum number of discordant reads required for each candidate fusion" value="2"/> | |
46 <param type="integer" name="x" label="Maximum number of breakpoints to examine for each pair of genomic regions" value="5"/> | |
47 <param type="integer" name="s" label="Minimum number of reads with the same breakpoint" value="1"/> | |
48 <param type="float" name="f" min="0" max="1" label="Minimum fraction of read bases required for alignment to fusion template" value=".9"/> | |
49 <param type="float" name="S" min="0" max="1" label="Minimum similarity required for read to match fusion template" value=".95"/> | |
50 <param type="integer" name="k" label="K-mer size (number of bases) for fragment comparison" value="10"/> | |
51 <param type="integer" name="c" label="Minimum size of soft-clipped region to consider" value="16"/> | |
52 <param type="integer" name="b" label="Number of bases flanking breakpoint for fusion template" value="500"/> | |
53 <param type="integer" name="p" label="Number of threads for blastn search" value="4"/> | |
54 <param type="integer" name="a" label="Number of bases flanking breakpoint to provide in output" value="50"/> | |
55 </when> | |
56 </conditional> | |
57 </inputs> | |
58 | |
59 <outputs> | |
60 <data format="tabular" name="outfile" /> | |
61 </outputs> | |
62 | |
63 <help>This tool does Factera</help> | |
64 | |
65 </tool> |