Mercurial > repos > iuc > jbrowse

annotate 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
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497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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1 <tool id="jbrowse" name="JBrowse" version="0.3">
0
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2 <description>genome browser</description>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <version_command>python jbrowse.py --version</version_command>
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9 <command interpreter="python"><![CDATA[jbrowse.py
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10 $positional_1
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11 $trackYaml
0
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12
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13 --jbrowse \${JBROWSE_SOURCE_DIR}
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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14 --outdir $default.files_path
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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15 > $default]]></command>
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16 <configfiles>
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17 <configfile name="trackYaml">
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18 ---
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19 #for $track in $data_tracks:
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20 -
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21 file: ${track.data_format.annotation}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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22 ext: ${track.data_format.annotation.ext}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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23 label: "${track.annotation_label}"
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24 category: "${track.category}"
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25 options:
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26 __unused__: "Not used...just to ensure options has at least one key"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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27 #if str($track.data_format.data_format_select) == "wiggle":
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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28 type: ${track.data_format.xyplot}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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29 variance_band: ${track.data_format.var_band}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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30 #if str($track.data_format.scaling.scale_select) == "auto_local":
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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31 autoscale: local
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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32 #else if str($track.data_format.scaling.scale_select) == "auto_global":
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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33 autoscale: global
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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34 #else:
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35 min: ${track.data_format.scaling.minimum}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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36 max: ${track.data_format.scaling.maximum}
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37 #end if
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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38 #else if str($track.data_format.data_format_select) == "pileup":
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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39 auto_snp: ${track.data_format.auto_snp}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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40 bam_index: ${track.data_format.annotation.metadata.bam_index}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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41 #else if str($track.data_format.data_format_select) == "blast":
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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42 parent: ${track.data_format.blast_parent}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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43 protein: ${track.data_format.is_protein}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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44 min_gap: ${track.data_format.min_gap}
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45 match: true
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46 #else if str($track.data_format.data_format_select) == "gene_calls":
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47 match: ${track.data_format.match_part}
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48 #end if
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49 #end for
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50 </configfile>
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51 </configfiles>
0
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52 <inputs>
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53 <param label="Genome" name="positional_1" type="data" format="fasta"/>
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54 <repeat name="data_tracks" title="Annotation Track">
1
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55 <param label="Track Label" name="annotation_label" type="text"/>
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56 <param label="Track Category" name="category" type="text" value="Default"
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57 help="Organise your tracks into Categories for a nicer end-user experience"/>
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58 <conditional name="data_format" label="Track Options">
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59 <param type="select" label="Track Type" name="data_format_select">
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60 <option value="gene_calls">GFF/GFF3/BED Featuers</option>
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61 <option value="pileup">BAM Pileups</option>
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62 <option value="blast">Blast XML</option>
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63 <option value="wiggle">BigWig XY</option>
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64 <option value="vcf">VCF SNPs</option>
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65 </param>
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66 <when value="blast">
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67 <param label="BlastXML Track Data" format="blastxml" name="annotation" type="data"/>
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68
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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."
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70 format="gff3" name="blast_parent" type="data"/>
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71
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72 <param label="Minimum Gap Size" help="before a new match_part feature is created" name="min_gap"
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73 type="integer" value="10" min="2" />
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74 <param label="Is this a protein blast search?"
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75 type="boolean" name="is_protein" truevalue="true" falsevalue="false" />
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76 </when>
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77 <when value="vcf">
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78 <param label="SNPs" help="in VCF"
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79 format="vcf" name="annotation" type="data"/>
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80 </when>
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81 <when value="gene_calls">
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82 <param label="Track Data" help="in GFF, GFF3, BED"
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83 format="gff,gff3,bed" name="annotation" type="data"/>
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84
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85 <param label="This is match/match_part data"
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86 type="boolean" name="match_part" truevalue="true" falsevalue="false" />
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87 </when>
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88 <when value="pileup">
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89 <param label="Track Data" help="in BAM"
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90 format="bam" name="annotation" type="data"/>
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91 <param label="Autogenerate SNP Track" help="Not recommended for deep coverage BAM files"
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92 type="boolean" name="auto_snp" truevalue="true" falsevalue="false" />
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93 </when>
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94 <when value="wiggle">
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95 <param label="Track Data" help="in BigWig"
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96 format="bigwig" name="annotation" type="data"/>
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97 <param label="Use XYPlot" help="instead of continuous coloured band"
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98 type="boolean" name="xyplot" truevalue="JBrowse/View/Track/Wiggle/XYPlot"
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99 falsevalue="JBrowse/View/Track/Wiggle/Density" />
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100 <param label="Show variance band" help="Only for XYPlots"
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101 type="boolean" name="var_band" truevalue="true"
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102 falsevalue="false" />
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103
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104 <conditional name="scaling" label="Scaling">
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105 <param type="select" label="Track Scaling" name="scale_select">
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106 <option value="auto_local">Autoscale (local)</option>
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107 <option value="auto_global">Autoscale (global)</option>
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108 <option vlue="fixed">Specify Min/Max</option>
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109 </param>
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110 <when value="auto_local"></when>
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111 <when value="auto_global"></when>
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112 <when value="fixed">
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113 <param label="Track minimum" name="minimum"
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114 type="integer" value="0" />
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115 <param label="Track maximum" name="maximum"
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116 type="integer" value="100" />
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117 </when>
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118 </conditional>
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119 </when>
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120 </conditional>
0
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121 </repeat>
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122 </inputs>
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123 <outputs>
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124 <data format="html" name="default" label="JBrowse on $positional_1.name"/>
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125 </outputs>
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126 <help><![CDATA[
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127 Deploy a static JBrowse visualization of a genome and some associated datasets
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128
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129 @ATTRIBUTION@
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130 ]]></help>
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131 <citations>
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132 <citation type="doi">10.1101/gr.094607.109</citation>
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133 </citations>
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134 </tool>
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135