Mercurial > repos > iuc > pilon

annotate pilon.xml @ 0:b362b0f74c78 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/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
author iuc
date Sat, 13 Aug 2016 04:33:19 -0400
parents
children 57cfa19f44ba
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
1 <tool id="pilon" name="pilon" version="0.1">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
2 <description>An automated genome assembly improvement and variant detection tool</description>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
3 <requirements>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
4 <requirement type="package" version="1.18">pilon</requirement>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
5 </requirements>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
7 #if $auto_selection.auto_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
8 #for $bamfile in $auto_selection.bam
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
9 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
10 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
11 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
12 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
13 #if $options.selection_mode == "advanced"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
14 #if $options.frags_selection.frags_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
15 #for $bamfile in $options.frags_selection.frags
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
16 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
17 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
18 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
19 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
20 #if $options.jumps_selection.jumps_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
21 #for $bamfile in $options.jumps_selection.jumps
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
22 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
23 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
24 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
25 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
26 #if $options.unpaired_selection.unpaired_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
27 #for $bamfile in $options.unpaired_selection.unpaired
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
28 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
29 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
30 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
31 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
32 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
33 ln -s -f
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
34 #if $reference_genome.reference_genome_source == "history"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
35 "$reference_genome.history_item"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
36 #else
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
37 "$reference_genome.builtin.fields.path"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
38 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
39 reference.fasta &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
40 pilon
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
41 --genome reference.fasta
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
42 $variant
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
43 $changes
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
44 #if $auto_selection.auto_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
45 #for $bamfile in $auto_selection.bam
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
46 --bam "\$(basename $bamfile)"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
47 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
48 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
49 #if $options.selection_mode == "advanced"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
50 #if $options.frags_selection.frags_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
51 #for $bamfile in $options.frags_selection.frags
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
52 --frags "\$(basename $bamfile)"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
53 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
54 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
55 #if $options.jumps_selection.jumps_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
56 #for $bamfile in $options.jumps_selection.jumps
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
57 --jumps "\$(basename $bamfile)"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
58 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
59 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
60 #if $options.unpaired_selection.unpaired_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
61 #for $bamfile in $options.unpaired_selection.unpaired
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
62 --unpaired "\$(basename $bamfile)"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
63 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
64 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
65 $options.vcfqe
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
66 $options.vcf
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
67 $options.tracks
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
68 --chunksize $options.chunk_size
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
69 $options.diploid
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
70 $options.duplicates
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
71 $options.iupac
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
72 $options.nonpf
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
73 #if len($options.targetlist.strip()) > 0
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
74 --targetlist $options.targetlist
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
75 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
76 --fix $options.fixes
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
77 $options.verbose
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
78 --defaultqual $options.defaultqual
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
79 --flank $options.flank
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
80 --gapmargin $options.gapmargin
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
81 --K $options.kmersize
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
82 --mindepth $options.mindepth
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
83 --mingap $options.mingap
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
84 --minmq $options.minmq
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
85 --minqual $options.minqual
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
86 $options.nostrays
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
87 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
88 --threads \${GALAXY_SLOTS:-1}
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
89 --output pilon
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
90 ]]></command>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
91 <inputs>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
92 <conditional name="reference_genome">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
93 <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
94 <option selected="True" value="history">Use a genome from history</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
95 <option value="builtin">Use a built-in genome"</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
96 </param>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
97 <when value="history">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
98 <param format="fasta" type="data" metadata_name="dbkey" name="history_item" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
99 </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
100 <when value="builtin">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
101 <param label="Select a reference genome" name="builtin" type="select">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
102 <options from_data_table="all_fasta">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
103 <filter column="2" type="sort_by" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
104 <validator message="No genomes are available for the selected input dataset" type="no_options" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
105 </options>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
106 </param>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
107 </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
108 </conditional>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
109 <conditional name="auto_selection">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
110 <param name="auto_enabled" label="Type automatically determined by pilon"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
111 type="boolean" checked="true" truevalue="yes" falsevalue="no" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
112 <when value="yes">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
113 <param argument="bam" label="Input BAM file" multiple="true" type="data" format="bam"/>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
114 </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
115 <when value="no"></when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
116 </conditional>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
117 <param argument="variant" type="boolean" label="Variant calling mode" checked="true" truevalue="--variant" falsevalue=""
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
118 help="Sets up heuristics for variant calling, as opposed to assembly improvement; equivalent to '--vcf --fix all,breaks'."/>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
119 <param argument="changes" type="boolean" label="Create changes file" truevalue="--changes" falsevalue=""
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
120 help="If specified, a file listing changes in the &lt;output&gt;.fasta will be generated."/>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
121 <conditional name="options">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
122 <param label="Use advanced options" name="selection_mode" type="select">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
123 <option selected="True" value="default">Use default options</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
124 <option value="advanced">Use advanced options</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
125 </param>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
126 <when value="default"> </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
127 <when value="advanced">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
128 <conditional name="frags_selection">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
129 <param name="frags_enabled" label="Paired end fragments" type="boolean" truevalue="yes" falsevalue="no" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
130 <when value="yes">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
131 <param argument="frags" label="Input BAM file (paired end fragments)" multiple="true" type="data" format="bam"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
132 help="BAM file consisting of fragment paired-end alignments." />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
133 </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
134 <when value="no"></when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
135 </conditional>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
136 <conditional name="jumps_selection">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
137 <param name="jumps_enabled" label="Mate pairs" type="boolean" truevalue="yes" falsevalue="no" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
138 <when value="yes">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
139 <param argument="jumps" label="Input BAM file (mate pairs)" multiple="true" type="data" format="bam"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
140 help="BAM file consisting of jump (mate pair) paired-end alignments." />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
141 </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
142 <when value="no"></when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
143 </conditional>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
144 <conditional name="unpaired_selection">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
145 <param name="unpaired_enabled" label="Unpaired reads" type="boolean" truevalue="yes" falsevalue="no" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
146 <when value="yes">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
147 <param argument="unpaired" label="Input BAM file (unpaired)" multiple="true" type="data" format="bam"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
148 help="BAM file consisting of unpaired alignments." />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
149 </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
150 <when value="no"></when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
151 </conditional>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
152 <param argument="vcf" type="boolean" checked="false" label="VCF output"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
153 truevalue="--vcf" falsevalue="" help="If specified, a vcf file will be generated (even if 'Variant calling mode' is off)"/>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
154 <param argument="tracks" type="boolean" checked="false" label="Output annotation tracks"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
155 help="Write many track files (*.bed, *.wig) suitable for viewing in a genome browser."
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
156 truevalue="--tracks" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
157 <param argument="chunk_size" type="integer" min="1" value="10000000" label="Chunk size"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
158 help="Input FASTA elements larger than this will be processed in smaller pieces not to
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
159 exceed this size." />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
160 <param argument="vcfqe" type="boolean" checked="false" label="QE (not QP) in VCF" help="If specified the VCF will contain a QE (quality-weighted evidence) field rather
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
161 than the default QP (quality-weighted percentage of evidence) field." truevalue="--vcfqe" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
162 <param argument="fixes" label="Issues that pilon should try and fix" type="select" multiple="true">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
163 <option value="all" selected="true">All non-experimental fixes</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
164 <option value="bases">Individual bases and small indels</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
165 <option value="gaps">Fill gaps</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
166 <option value="local">Detect and fix local misassemblies</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
167 <option value="none">Do none of these fixes (no FASTA will be written)</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
168 <option value="amb">Fix ambigious bases in FASTA output (experimental)</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
169 <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
170 <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
171 </param>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
172 <param argument="diploid" label="Organism is diploid" type="boolean" checked="false"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
173 help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
174 truevalue="--diploid" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
175 <param argument="duplicates" label="Use duplicates" type="boolean" checked="false"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
176 help="Use reads marked as duplicates in the input BAMs"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
177 truevalue="--duplicates" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
178 <param argument="iupac" label="Use IUPAC codes in FASTA output" type="boolean" checked="false"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
179 help="Output IUPAC ambiguous base codes in the output FASTA file when appropriate"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
180 truevalue="--iupac" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
181 <param argument="nonpf" label="Use low quality reads" type="boolean" checked="false"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
182 help="Use reads which failed sequencer quality filtering"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
183 truevalue="--nonpf" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
184 <param argument="targetlist" label="List of targets to process (leave blank for all)" default="" type="text" length="40"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
185 help="Only process the specified target(s). Targets are comma-separated, and each target is a fasta element name optionally followed by a base range." />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
186 <param argument="verbose" label="Verbose output (in tool log)" type="boolean" check="false"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
187 truevalue="--verbose" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
188 <param argument="defaultqual" label="Default base quality" type="integer" min="1" value="15"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
189 help="Assumes bases are of this quality if quals are no present in input BAMs" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
190 <param argument="flank" label="Flanking bases to ignore" type="integer" min="1" value="10"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
191 help="This many bases at each end of the good reads will be ignored." />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
192 <param argument="gapmargin" label="Allowable gap margin" type="integer" min="1" value="100000"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
193 help="Closed gaps must be within this number of bases of true size to be closed" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
194 <param argument="kmersize" label="Kmer size" type="integer" min="1" value="47"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
195 help="Kmer size used by internal assembler" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
196 <param argument="mindepth" label="Minimum depth" type="float" value="0.1"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
197 help="Minimum depth of coverage required for variants to be called. See complete documentation below." />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
198 <param argument="mingap" label="Mininum gap size" type="integer" value="10"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
199 help="Minimum size for unclosed gaps" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
200 <param argument="minmq" label="Minimum mapping quality" type="integer" value="0"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
201 help="Minimum alignment mapping quality for a read to count in pileups" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
202 <param argument="minqual" label="Minimum base quality" type="integer" value="0"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
203 help="Minimum base quality to consider for pileups" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
204 <param argument="nostrays" label="Disable 'stray read filtering'" type="boolean" checked="false"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
205 help="See documentation below"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
206 truevalue="--nostrays" falsevalue="" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
207 </when>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
208 </conditional>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
209 </inputs>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
210 <outputs>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
211 <data format="vcf" from_work_dir="pilon.vcf" label="VCF from ${tool.name} on ${on_string}" name="output_vcf">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
212 <filter>variant or (options['selection_mode'] == 'advanced' and options['vcf'])</filter>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
213 </data>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
214 <data format="txt" from_work_dir="pilon.changes" label="Changes in FASTA from ${tool.name} on ${on_string}" name="output_changes">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
215 <filter>changes</filter>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
216 </data>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
217 <data format="fasta" from_work_dir="pilon.fasta" label="FASTA from ${tool.name} on ${on_string}" name="output_fasta">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
218 <filter>options['selection_mode'] == 'default' or (options['selection_mode'] == 'advanced' and 'none' not in options['fixes'])</filter>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
219 </data>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
220 <collection name="tracks" type="list" label="Annotation tracks from ${tool.name} on ${on_string}">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
221 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
222 <data format="bed" from_work_dir="pilonPilon.bed" label="Features from ${tool.name} on ${on_string} (BED format)" name="output_pilon_bed" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
223 <data format="wig" from_work_dir="pilonChanges.wig" label="${tool.name} changes track on ${on_string} (WIG format)" name="output_changes_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
224 <data format="wig" from_work_dir="pilonUnconfirmed.wig" label="${tool.name} unconfirmed track on ${on_string}" name="output_unconfirmed_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
225 <data format="wig" from_work_dir="pilonCopyNumber.wig" label="${tool.name} copy number track on ${on_string}" name="output_copynumber_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
226 <data format="wig" from_work_dir="pilonCoverage.wig" label="${tool.name} coverage track on ${on_string}" name="output_coverage_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
227 <data format="wig" from_work_dir="pilonBadCoverage.wig" label="${tool.name} bad coverage track on ${on_string}" name="output_badcoverage_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
228 <data format="wig" from_work_dir="pilonPctBad.wig" label="${tool.name} pct bad track on ${on_string}" name="output_pctbad_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
229 <data format="wig" from_work_dir="pilonDeltaCoverage.wig" label="${tool.name} delta coverage track on ${on_string}" name="output_deltacoverage_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
230 <data format="wig" from_work_dir="pilonDipCoverage.wig" label="${tool.name} dip coverage track on ${on_string}" name="output_dipcoverage_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
231 <data format="wig" from_work_dir="pilonPhysicalCoverage.wig" label="${tool.name} physical coverage track on ${on_string}" name="output_physicalcoverage_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
232 <data format="wig" from_work_dir="pilonClippedAlignments.wig" label="${tool.name} clipped alignments track on ${on_string}" name="output_clippedalignments_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
233 <data format="wig" from_work_dir="pilonWeightedQual.wig" label="${tool.name} weighted quality track on ${on_string}" name="output_weightedqual_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
234 <data format="wig" from_work_dir="pilonWeightedMq.wig" label="${tool.name} weighted MQ track on ${on_string}" name="output_weightedmq_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
235 <data format="wig" from_work_dir="pilonGC.wig" label="${tool.name} GC track on ${on_string}" name="output_gc_wig" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
236 </collection>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
237 </outputs>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
238 <tests>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
239 <test>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
240 <param name="reference_genome_source" value="history" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
241 <param ftype="fasta" name="history_item" value="test1.fasta" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
242 <param name="bam" value="test1.bam" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
243 <param name="variant" value="true" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
244 <output file="test1-vcf-part" ftype="vcf" name="output_vcf" compare="contains" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
245 <output md5="352907b0d965bc926289b1b2eb9cbecb" ftype="fasta" name="output_fasta" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
246 </test>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
247 <test>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
248 <param name="reference_genome_source" value="history" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
249 <param ftype="fasta" name="history_item" value="test1.fasta" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
250 <param name="bam" value="test1.bam" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
251 <param name="variant" value="true" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
252 <param name="selection_mode" value="advanced" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
253 <param name="tracks" value="true" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
254 <output file="test1-vcf-part" ftype="vcf" name="output_vcf" compare="contains" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
255 <output md5="352907b0d965bc926289b1b2eb9cbecb" ftype="fasta" name="output_fasta" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
256 <output_collection name="tracks">
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
257 <element name="output_pilon_bed" md5="ae0518a6d641efecdcf41c808c014226" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
258 <element name="output_changes_wig" md5="26e0a9a3793e6604673e9911c4d334ab" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
259 <element name="output_unconfirmed_wig" md5="f8bb3def4547e854bd90e1a6b4f8cc66" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
260 <element name="output_copynumber_wig" md5="c1e94296fbc24d00fa7d057f30e4de8f" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
261 <element name="output_coverage_wig" md5="48f7da4bad60fcbb49aaaa992aef8a02" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
262 <element name="output_badcoverage_wig" md5="31e3ad4a5d0f8cd1e296e4b1424d6a95" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
263 <element name="output_pctbad_wig" md5="8353134113c87dbc7d9497f983d58b4b" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
264 <element name="output_deltacoverage_wig" md5="e0fb6474b851e1890f91c57c2ba1fd76" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
265 <element name="output_dipcoverage_wig" md5="8885c63df1dc7309a7bab371b9eb449b" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
266 <element name="output_physicalcoverage_wig" md5="db485f84b51499c3a3c72da70a8ef7af" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
267 <element name="output_clippedalignments_wig" md5="b6eab0827a9b6f2e925d9ece5ee4f87f" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
268 <element name="output_weightedqual_wig" md5="9987289bd0ec8cd05bd6d330bdd1d01d" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
269 <element name="output_weightedmq_wig" md5="7ec1b6420f52fc44bf3c04aa593fcdeb" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
270 <element name="output_gc_wig" md5="815af1378d016b85ed6f52667dde10c1" />
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
271 </output_collection>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
272 </test>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
273
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
274 </tests>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
275 <help><![CDATA[
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
276 Pilon is a software tool which can be used to:
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
277
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
278 * Automatically improve draft assemblies
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
279
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
280 * Find variation among strains, including large event detection
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
281
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
282 Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
283
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
284 * Single base differences
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
285
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
286 * Small indels
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
287
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
288 * Larger indel or block substitution events
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
289
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
290 * Gap filling
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
291
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
292 * Identification of local misassemblies, including optional opening of new gaps
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
293
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
294 Pilon then outputs a FASTA file containing an improved representation of the genome from the read data and an optional VCF file detailing variation seen between the read data and the input genome.
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
295
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
296 To aid manual inspection and improvement by an analyst, Pilon can optionally produce tracks that can be displayed in genome viewers such as IGV and GenomeView, and it reports other events (such as possible large collapsed repeat regions) in its standard output.
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
297
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
298 Note on **mindepth**:
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
299
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
300 Variants (snps and indels) will only be called if there is coverage of good pairs
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
301 at the value set for *mindepth* depth or more; if this value is >= 1, it is an absolute depth, if it is a
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
302 fraction < 1, then minimum depth is computed by multiplying this value by the mean
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
303 coverage for the region, with a minumum value of 5 (default 0.1: min depth to call
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
304 is 10% of mean coverage or 5, whichever is greater).
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
305
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
306 Note on **stray read filtering**
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
307
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
308 By default a pass is made through the input BAM files to identify stray pairs, that is,
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
309 those pairs in which both reads are aligned but not marked valid because they have
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
310 inconsistent orientation or separation. Identifying stray pairs can help fill gaps
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
311 and assemble larger insertions, especially of repeat content. However, doing so
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
312 sometimes consumes considerable memory.
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
313 ]]></help>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
314 <citations>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
315 <citation type="doi">10.1371/journal.pone.0112963</citation>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
316 </citations>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
iuc
parents:
diff changeset
317 </tool>