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comparison jbrowse.xml @ 1:497c6bb3b717 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
author iuc
date Thu, 18 Jun 2015 12:10:51 -0400
parents 2c9e5136b416
children 7342f467507b
comparison
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0:2c9e5136b416 1:497c6bb3b717
1 <tool id="jbrowse" name="JBrowse" version="0.1"> 1 <tool id="jbrowse" name="JBrowse" version="0.3">
2 <description>genome browser</description> 2 <description>genome browser</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <version_command>python jbrowse.py --version</version_command> 8 <version_command>python jbrowse.py --version</version_command>
9 <command interpreter="python"><![CDATA[jbrowse.py 9 <command interpreter="python"><![CDATA[jbrowse.py
10 $positional_1 10 $positional_1
11 11 $trackYaml
12 #set data_files = '" "'.join([ str($var.gff3) for $var in $data_tracks ])
13 #set data_formats = '" "'.join([ str($var.gff3.ext) for $var in $data_tracks ])
14 #set data_labels = '" "'.join([ str($var.gff3_label) for $var in $data_tracks ])
15
16 --gff3 "$data_files"
17 --gff3_format "$data_formats"
18 --gff3_label "$data_labels"
19
20 12
21 --jbrowse \${JBROWSE_SOURCE_DIR} 13 --jbrowse \${JBROWSE_SOURCE_DIR}
22 --outdir $default.files_path 14 --outdir $default.files_path
23 > $default]]></command> 15 > $default]]></command>
16 <configfiles>
17 <configfile name="trackYaml">
18 ---
19 #for $track in $data_tracks:
20 -
21 file: ${track.data_format.annotation}
22 ext: ${track.data_format.annotation.ext}
23 label: "${track.annotation_label}"
24 category: "${track.category}"
25 options:
26 __unused__: "Not used...just to ensure options has at least one key"
27 #if str($track.data_format.data_format_select) == "wiggle":
28 type: ${track.data_format.xyplot}
29 variance_band: ${track.data_format.var_band}
30 #if str($track.data_format.scaling.scale_select) == "auto_local":
31 autoscale: local
32 #else if str($track.data_format.scaling.scale_select) == "auto_global":
33 autoscale: global
34 #else:
35 min: ${track.data_format.scaling.minimum}
36 max: ${track.data_format.scaling.maximum}
37 #end if
38 #else if str($track.data_format.data_format_select) == "pileup":
39 auto_snp: ${track.data_format.auto_snp}
40 bam_index: ${track.data_format.annotation.metadata.bam_index}
41 #else if str($track.data_format.data_format_select) == "blast":
42 parent: ${track.data_format.blast_parent}
43 protein: ${track.data_format.is_protein}
44 min_gap: ${track.data_format.min_gap}
45 match: true
46 #else if str($track.data_format.data_format_select) == "gene_calls":
47 match: ${track.data_format.match_part}
48 #end if
49 #end for
50 </configfile>
51 </configfiles>
24 <inputs> 52 <inputs>
25 <param label="Genome" name="positional_1" type="data" format="fasta"/> 53 <param label="Genome" name="positional_1" type="data" format="fasta"/>
26 <repeat name="data_tracks" title="Annotation Track"> 54 <repeat name="data_tracks" title="Annotation Track">
27 <param label="Annotation Data" help="in GFF, GFF3, or BED formats" 55 <param label="Track Label" name="annotation_label" type="text"/>
28 format="gff,gff3,bed" name="gff3" type="data"/> 56 <param label="Track Category" name="category" type="text" value="Default"
29 <param label="Dataset Label" name="gff3_label" type="text"/> 57 help="Organise your tracks into Categories for a nicer end-user experience"/>
58 <conditional name="data_format" label="Track Options">
59 <param type="select" label="Track Type" name="data_format_select">
60 <option value="gene_calls">GFF/GFF3/BED Featuers</option>
61 <option value="pileup">BAM Pileups</option>
62 <option value="blast">Blast XML</option>
63 <option value="wiggle">BigWig XY</option>
64 <option value="vcf">VCF SNPs</option>
65 </param>
66 <when value="blast">
67 <param label="BlastXML Track Data" format="blastxml" name="annotation" type="data"/>
68
69 <param label="Features used in Blast Search" help="in GFF3. This is required so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file."
70 format="gff3" name="blast_parent" type="data"/>
71
72 <param label="Minimum Gap Size" help="before a new match_part feature is created" name="min_gap"
73 type="integer" value="10" min="2" />
74 <param label="Is this a protein blast search?"
75 type="boolean" name="is_protein" truevalue="true" falsevalue="false" />
76 </when>
77 <when value="vcf">
78 <param label="SNPs" help="in VCF"
79 format="vcf" name="annotation" type="data"/>
80 </when>
81 <when value="gene_calls">
82 <param label="Track Data" help="in GFF, GFF3, BED"
83 format="gff,gff3,bed" name="annotation" type="data"/>
84
85 <param label="This is match/match_part data"
86 type="boolean" name="match_part" truevalue="true" falsevalue="false" />
87 </when>
88 <when value="pileup">
89 <param label="Track Data" help="in BAM"
90 format="bam" name="annotation" type="data"/>
91 <param label="Autogenerate SNP Track" help="Not recommended for deep coverage BAM files"
92 type="boolean" name="auto_snp" truevalue="true" falsevalue="false" />
93 </when>
94 <when value="wiggle">
95 <param label="Track Data" help="in BigWig"
96 format="bigwig" name="annotation" type="data"/>
97 <param label="Use XYPlot" help="instead of continuous coloured band"
98 type="boolean" name="xyplot" truevalue="JBrowse/View/Track/Wiggle/XYPlot"
99 falsevalue="JBrowse/View/Track/Wiggle/Density" />
100 <param label="Show variance band" help="Only for XYPlots"
101 type="boolean" name="var_band" truevalue="true"
102 falsevalue="false" />
103
104 <conditional name="scaling" label="Scaling">
105 <param type="select" label="Track Scaling" name="scale_select">
106 <option value="auto_local">Autoscale (local)</option>
107 <option value="auto_global">Autoscale (global)</option>
108 <option vlue="fixed">Specify Min/Max</option>
109 </param>
110 <when value="auto_local"></when>
111 <when value="auto_global"></when>
112 <when value="fixed">
113 <param label="Track minimum" name="minimum"
114 type="integer" value="0" />
115 <param label="Track maximum" name="maximum"
116 type="integer" value="100" />
117 </when>
118 </conditional>
119 </when>
120 </conditional>
30 </repeat> 121 </repeat>
31 </inputs> 122 </inputs>
32 <outputs> 123 <outputs>
33 <data format="html" name="default" label="JBrowse on $positional_1.name"/> 124 <data format="html" name="default" label="JBrowse on $positional_1.name"/>
34 </outputs> 125 </outputs>