Mercurial > repos > mvdbeek > yaha

annotate yaha.xml @ 0:0c888a0686bb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
author mvdbeek
date Thu, 29 Dec 2016 14:51:49 -0500
parents
children 584220a3c520
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
1 <tool id="yaha" name="yaha" version="0.1.83">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
2 <description>fast and flexible long-read alignment with optimal breakpoint detection</description>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
3 <macros>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
4 <import>macros.xml</import>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
5 </macros>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
6 <requirements>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
7 <requirement type="package" version="0.1.83">yaha</requirement>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
8 <requirement type="package" version="0.6.5">sambamba</requirement>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
9 </requirements>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
10 <version_command><![CDATA[yaha 2>&1| head -n1]]></version_command>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
11 <command detect_errors="aggressive"><![CDATA[
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
12 #if $reference_genome.reference_genome_source == "history" or "reference":
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
13 #if $reference_genome.reference_genome_source == "history":
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
14 ln -f -s "$reference_genome.history_item" genome.fa &&
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
15 #elif $reference_genome.reference_genome_source == "reference":
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
16 ln -f -s "$reference_genome.fasta_item" genome.fa &&
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
17 #end if
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
18 yaha -g genome.fa -H $reference_genome.maxHitsIndex -L $reference_genome.wordLenIndex -S $reference_genome.skipDistanceIndex &&
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
19 #set maxHitsIndex = "%s%s" % ("0" * (5 - len(str($reference_genome.maxHitsIndex))), $reference_genome.maxHitsIndex)
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
20 #set skipdist = $reference_genome.skipDistanceIndex if len(str($reference_genome.skipDistanceIndex)) > 1 else "0%s" % $reference_genome.skipDistanceIndex
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
21 #set wordLenIndex = $reference_genome.wordLenIndex if len(str($reference_genome.wordLenIndex)) > 1 else "0%s" % $reference_genome.wordLenIndex
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
22 #set index_path = "genome.X%s_%s_%sS" % ($wordLenIndex, $skipdist, $maxHitsIndex)
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
23 #else:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
24 #pass ## augment with pre-built index if considered useful
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
25 #end if
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
26 yaha
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
27 -x '$index_path'
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
28 -q '$q'
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
29 $outformat stdout
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
30 -t \${GALAXY_SLOTS:-1}
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
31 -BW $BW
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
32 -G $G
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
33 -H $H
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
34 -M $M
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
35 -MD $MD
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
36 -P $P
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
37 -X $X
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
38 #if $ags.use_ags == "yes":
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
39 -AGS Y
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
40 -GEC $ags.GEC
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
41 -GOC $ags.GOC
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
42 -MS $ags.MS
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
43 -RC $ags.RC
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
44 #else:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
45 -AGS N
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
46 #end if
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
47 #if $oqc.use_oqc == "yes":
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
48 -OQC Y
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
49 -BP $oqc.BP
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
50 -MGDP $oqc.MGDP
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
51 -MNO $oqc.MNO
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
52 #else:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
53 -OQC N
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
54 #end if
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
55 #if $fbs.use_fbs == "yes":
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
56 -FBS Y
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
57 -PRL $fbs.PRL
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
58 -PSS $fbs.PSS
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
59 #else:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
60 -FBS N
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
61 #end if
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
62 | sambamba view -S -f bam /dev/stdin | sambamba sort -o '$alignment' -l 6 -t \${GALAXY_SLOTS:-1} /dev/stdin
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
63 ]]></command>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
64 <inputs>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
65 <param type="data" argument="q" label="Fastq reads to align" format="fastqsanger" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
66 <conditional name="reference_genome">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
67 <param help="Built-in references were created using default options" label="Source for the reference genome to align against" name="reference_genome_source" type="select">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
68 <!-- Write a datamanager if prebuilt genomes are important
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
69 <option selected="True" value="indexed">Use a built-in index</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
70 -->
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
71 <option value="history">Use a genome from history to build an index</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
72 <option value="reference">Use a built-in genome to build an index</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
73 </param>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
74 <when value="indexed">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
75 <param help="If your genome of interest is not listed, contact the Galaxy team" label="Select a reference genome" name="index" type="select">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
76 <options from_data_table="yaha_indexes">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
77 <filter column="2" type="sort_by" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
78 <validator message="No genomes are available for the selected input dataset" type="no_options" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
79 </options>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
80 </param>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
81 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
82 <when value="history">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
83 <param format="fasta" label="Select the reference genome" name="history_item" type="data" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
84 <expand macro="index_parameter"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
85 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
86 <when value="reference">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
87 <param label="Select a reference genome" name="fasta_item" type="select">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
88 <options from_data_table="fasta_indexes">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
89 <filter column="2" type="sort_by"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
90 </options>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
91 </param>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
92 <expand macro="index_parameter"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
93 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
94 </conditional>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
95 <param name="outformat" type="select" label="Produce alignment with softclipping?">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
96 <option value="-osh">Produce alignment with hard clipping</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
97 <option value="-oss">Produce alignment with soft clipping</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
98 </param>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
99 <param type="integer" argument="-BW" value="5" min="0" label="BandWidth" help="band size on each side of the diagonal of banded Smith Waterman" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
100 <param type="integer" argument="-G" value="50" min="0" label="maxGap" help="maximum indel size allowed with a single alignment" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
101 <param type="integer" argument="-H" value="650" min="1" max="65525" label="maxHits" help="maximum times a seed is in the reference before it is ignored as too repetitive. To take advantage of k-mer sampling, use the same value of maxHits during index creation and alignment." />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
102 <param type="integer" argument="-M" value="25" min="0" label="minMatch" help="minimum number of bases in seeds to start an alignment" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
103 <param type="integer" argument="-MD" value="50" min="0" label="MaxDesert" help="maximum number of contiguous bases without a seed before alignmment is split" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
104 <param type="float" argument="-P" value="0.9" min="0" label="minPercent-identity" help="minimum matching/alignment-length for a query to be included in output" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
105 <param type="integer" argument="-X" value="25" min="0" label="Xdropoff" help="maximum score dropoff before terminating alignment extensions" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
106 <conditional name="ags">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
107 <param name="use_ags" type="select" label="Use Affine Gap Scoring?">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
108 <option value="yes" selected="True">Yes</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
109 <option value="no">No</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
110 </param>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
111 <when value="yes">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
112 <param argument="-GEC" type="integer" value="2" min="0" label="GapExtensionCost" help="cost for extending a gap (indel)"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
113 <param argument="-GOC" type="integer" value="5" min="0" label="GapOpenCost" help="cost for starting a new gap (indel)"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
114 <param argument="-MS" type="integer" value="1" min="0" label="MatchScore" help="score added for each matching base"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
115 <param argument="-RC" type="integer" value="3" min="0" label="ReplacementCost" help="score subtracted for each mismatched base"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
116 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
117 <when value="no">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
118 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
119 </conditional>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
120 <conditional name="oqc">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
121 <param name="use_oqc" type="select" label="Use Optimal Query Coverage Algorithm?" help="">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
122 <option value="yes" selected="True">Yes (Find a set of alignments are found that optimally cover the query, using the remaining options)</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
123 <option value="no">No (Output all alignments meeting above criteria)</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
124 </param>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
125 <when value="yes">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
126 <param argument="-BP" type="integer" value="5" min="0" label="BreakpointPenalty" help="penalty for inserting a breakpoint in split-read alignment"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
127 <param argument="-MGDP" type="integer" value="5" min="0" label="MaxGenomicDistancePenalty"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
128 <param argument="-MNO" type="integer" value="25" min="0" label="MinNonOverlap" help="minimum number of unshared bases required in each split alignment"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
129 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
130 <when value="no">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
131 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
132 </conditional>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
133 <conditional name="fbs">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
134 <param name="use_fbs" type="select" label="Use Filter By Similarity Algorithm?" help="">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
135 <option value="yes" selected="False">Yes (Output alignments similar to best alignment found using OQC.)</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
136 <option value="no">No</option>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
137 </param>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
138 <when value="yes">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
139 <param argument="-PRL" type="float" value="0.9" min="0" max="1" label="PercentReciprocalLength" help="minimum ratio of overlapping length between similar alignment"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
140 <param argument="-PSS" type="float" value="0.9" min="0" max="1" label="PercentSimilarScore" help="minimum ratio of scores between similar alignments"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
141 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
142 <when value="no">
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
143 </when>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
144 </conditional>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
145 </inputs>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
146 <outputs>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
147 <data name="alignment" format="bam" />
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
148 </outputs>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
149 <tests>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
150 <test>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
151 <param name="q" value="input.fastq" ftype="fastqsanger"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
152 <param name="reference_genome_source" value="history"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
153 <param name="history_item" value="phiX.fa" ftype="fasta"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
154 <output name="alignment" value="alignment.bam" ftype="bam"/>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
155 </test>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
156 </tests>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
157 <help><![CDATA[
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
158 Summary
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
159 -------
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
160
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
161 *yaha* is an open source, flexible, sensitive and accurate DNA aligner
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
162 designed for single-end reads. It supports three major modes of
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
163 operation:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
164
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
165 1. The default “Optimal Query Coverage” (**-OQC**) mode reports the best
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
166 set of alignments that cover the length of each query.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
167 2. Using “Filter By Similarity” (**-FBS**), along with the best set of
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
168 alignments, *yaha* will also output alignments that are highly
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
169 similar to an alignment in the best set.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
170 3. Finally, *yaha* can output all the alignments found for each query.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
171
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
172 The **-OQC** and **-FBS** modes are specifically tuned to form split
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
173 read mappings that can be used to accurately identify structural
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
174 variation events (deletions, duplications, insertions or inversions)
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
175 between the subject query and the reference genome.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
176
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
177 Usage
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
178 -----
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
179
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
180 **OPTIONS:** Default values enclosed in square brackets []
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
181
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
182 ::
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
183
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
184 Input/Output Options:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
185 -g FILE input genome file to use during index creation (FASTA or nib2)
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
186 -q FILE input file of sequence reads to align (FASTA or FASTQ) [STDIN]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
187 -osh FILE output file for alignment output in SAM format with hard clipping(default) [STDOUT]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
188 -oss FILE output file for alignment output in SAM format with soft clipping [STDOUT]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
189 -x FILE reference index file to use during alignment
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
190 NOTE: At most one of -osh or -oss should be specified.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
191
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
192 Index Creation Options:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
193 -H INT maxHits: During index creation, seeds occuring more than maxHits times will be sampled [65565]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
194 -L INT seedLength: Length of seed to use. During alignment, seed length is taken from index file [15]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
195 -S INT Skipdistance: Number of bases to skip ahead before forming next seed [1]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
196
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
197 General Alignment Options:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
198 -BW INT BandWidth: band size on each side of the diagonal of banded Smith Waterman [5]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
199 -G INT maxGap: maximum indel size allowed with a single alignment [50]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
200 -H INT maxHits: maximum times a seed is in the reference before it is ignored as too repetitive [650]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
201 -M INT minMatch: minimum number of bases in seeds to start an alignment [25]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
202 -MD INT MaxDesert: maximum number of contiguous bases without a seed before alignmment is split [50]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
203 -P REAL minPercent-identity: minimum matching/alignment-length for a query to be included in output [0.9]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
204 -X INT Xdropoff: maximum score dropoff before terminating alignment extensions [25]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
205 -t INT numThreads: number of threads used to parallel process reads [1]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
206
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
207 Affine Gap Scoring Options:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
208 If -AGS is off, a simple edit distance calculation is done.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
209 If on, the remaining options are used:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
210 -AGS BOOL (Y|N) controls use of Affine Gap Scoring [Y].
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
211 -GEC INT GapExtensionCost: cost for extending a gap (indel) [2]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
212 -GOC INT GapOpenCost: cost for starting a new gap (indel) [5]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
213 -MS INT MatchScore: score added for each matching base [1]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
214 -RC INT ReplacementCost: score subtracted for each mismatched base [3]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
215
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
216 Optimal Query Coverage Options:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
217 If -OQC if off, all alignments meeting above criteria are output.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
218 If -OQC is on, a set of alignments are found that optimally cover the query, using the remaining options.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
219 -OQC BOOL (Y|N) controls use of the Optimal Query Coverage Algorithm.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
220 -BP INT BreakpointPenalty: penalty for inserting a breakpoint in split-read alignment [5]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
221 -MGDP INT MaxGenomicDistancePenalty (5)]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
222 -MNO INT MinNonOverlap: minimum number of unshared bases required in each split alignment [minMatch]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
223 NOTE: The total cost of adding a breakpoint in a split-read mapping is:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
224 BP*MIN(MGDP, Log10(genomic distance between reference loci))
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
225
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
226 Filter By Similarity Options:
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
227 If -FBS is on, the remaining options are used. An alignemnt must satisfy BOTH criteria to be "similar".
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
228 -FBS BOOL (Y|N) controls output of alignments similar to best alignment found using OQC.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
229 -PRL REAL PercentReciprocalLength: minimum ratio of overlapping length between similar alignemnt [0.9]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
230 -PSS REAL PercentSimilarScore: minimum ratio of scores between similar alignments [0.9]
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
231
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
232 See the `User Guide <https://www.dropbox.com/s/7j758vpbaskcq20/YAHA_User_Guide.0.1.83.pdf?dl=0>`__
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
233 for more details on all options and their usage.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
234
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
235 | **Written by:** Greg Faust (gf4ea@virginia.edu)
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
236 | `Ira Hall Lab, University of
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
237 Virginia <http://faculty.virginia.edu/irahall/>`__
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
238
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
239 | **Please cite:**
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
240 | `Faust G.G. and Hall I.M., "*YAHA*: fast and flexible long-read
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
241 alignment with optimal breakpoint detection," *Bioinformatics* Oct.
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
242 2012; **28**\ (19):
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
243 2417-2424. <http://bioinformatics.oxfordjournals.org/content/28/19/2417>`__
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
244 ]]></help>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
245 <citations>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
246 <citation type="doi">10.1093/bioinformatics/bts456</citation>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
247 </citations>
0c888a0686bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 15b31d03f0dbc59ec544d4ce5837ff03b6936c27-dirty
mvdbeek
parents:
diff changeset
248 </tool>