Mercurial > repos > iuc > jbrowse
annotate macros.xml @ 3:7342f467507b draft
Uploaded v0.4 of JBrowse
| author | iuc |
|---|---|
| date | Thu, 31 Dec 2015 13:58:43 -0500 |
| parents | b6a0e126dbee |
| children | ae9382cfb6ac |
| rev | line source |
|---|---|
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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1 <?xml version="1.0"?> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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changeset
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2 <macros> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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3 <xml name="requirements"> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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4 <requirements> |
| 3 | 5 <requirement type="package" version="1.12.0">jbrowse</requirement> |
| 6 <requirement type="package" version="1.12.0">bundle_jbrowse</requirement> | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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7 <requirement type="package" version="2.7">python</requirement> |
| 3 | 8 <requirement type="package" version="5.18.1">perl</requirement> |
| 9 <requirement type="package" version="1.66">biopython</requirement> | |
| 10 <requirement type="package" version="0.6.2">bcbiogff</requirement> | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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11 <requirement type="package" version="1.2">samtools</requirement> |
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b6a0e126dbee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a9cedb0983cc262cfdac04464566fdded884318b
iuc
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12 <requirement type="package" version="3.11">pyyaml</requirement> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
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13 <yield/> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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14 </requirements> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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15 </xml> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
changeset
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16 <token name="@WRAPPER_VERSION@">1.0</token> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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17 <xml name="stdio"> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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18 <stdio> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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19 <exit_code range="1:"/> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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20 <exit_code range=":-1"/> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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21 <regex match="Error:"/> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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22 <regex match="Exception:"/> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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23 </stdio> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
24 </xml> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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25 <token name="@ATTRIBUTION@"><![CDATA[ |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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26 **Attribution** |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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27 |
| 3 | 28 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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29 ]]> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
30 </token> |
| 3 | 31 <xml name="auto_manual_tk" |
| 32 token_cond_label="Color" | |
| 33 token_cond_name="color" | |
| 34 token_select_label="Color Specification" | |
| 35 token_select_name="color_select" | |
| 36 token_automatic_label="Automatically selected" | |
| 37 token_manual_label="Manual Color Selection"> | |
| 38 <conditional name="@COND_NAME@" label="@COND_LABEL@"> | |
| 39 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@"> | |
| 40 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> | |
| 41 <option value="manual">@MANUAL_LABEL@</option> | |
| 42 </param> | |
| 43 <when value="automatic"> | |
| 44 </when> | |
| 45 <when value="manual"> | |
| 46 <yield /> | |
| 47 </when> | |
| 48 </conditional> | |
| 49 </xml> | |
| 50 | |
| 51 <xml name="jb_color" | |
| 52 token_label="JBrowse style.color" | |
| 53 token_name="style_color" | |
| 54 token_value="goldenrod" | |
| 55 token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS" | |
| 56 > | |
| 57 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@"> | |
| 58 <sanitizer> | |
| 59 <valid initial="string.letters,string.digits"> | |
| 60 <add value="#" /> | |
| 61 </valid> | |
| 62 </sanitizer> | |
| 63 </param> | |
| 64 </xml> | |
| 65 | |
| 66 <xml name="auto_color" | |
| 67 token_cond_label="Color" | |
| 68 token_cond_name="color" | |
| 69 token_select_label="Color Selection" | |
| 70 token_select_name="color_select" | |
| 71 token_automatic_label="Automatically selected" | |
| 72 token_manual_label="Manual Color Selection"> | |
| 73 <expand macro="auto_manual_tk" | |
| 74 cond_label="@COND_LABEL@" | |
| 75 cond_name="@COND_NAME@" | |
| 76 select_label="@SELECT_LABEL@" | |
| 77 select_name="@SELECT_NAME@" | |
| 78 automatic_label="@AUTOMATIC_LABEL@" | |
| 79 manual_label="@MANUAL_LABEL@"> | |
| 80 <expand macro="jb_color" /> | |
| 81 <yield /> | |
| 82 </expand> | |
| 83 </xml> | |
| 84 | |
| 85 | |
| 86 | |
| 87 <xml name="brewer_scheme"> | |
| 88 <param type="select" label="Brewer color Scheme" name="brewer_scheme"> | |
| 89 <option value="BrBg">BrBg: Brown - Blue Green</option> | |
| 90 <option value="PiYg">PiYg: Pink - Yellow Green</option> | |
| 91 <option value="PRGn">PRGn: Purple Red - Green</option> | |
| 92 <option value="PuOr">PuOr: Purple - Orange</option> | |
| 93 <option value="RdBu" selected="true">RdBu: Red - Blue</option> | |
| 94 <option value="RdGy">RdGy: Red - Gray</option> | |
| 95 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> | |
| 96 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> | |
| 97 <option value="Spectral">Spectral</option> | |
| 98 </param> | |
| 99 </xml> | |
| 100 <xml name="color_selection_minmax"> | |
| 101 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> | |
| 102 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the | |
| 103 auto case as well, but may be safe to just say "brewer colors? Pff, | |
| 104 red/blue" --> | |
| 105 <expand macro="auto_manual_tk" | |
| 106 token_cond_label="Color" | |
| 107 token_cond_name="color" | |
| 108 token_select_label="Color Selection" | |
| 109 token_select_name="color_select" | |
| 110 token_automatic_label="Automatically selected" | |
| 111 token_manual_label="Manual Color Selection"> | |
| 112 <expand macro="jb_color" | |
| 113 label="JBrowse style.pos_color" | |
| 114 name="style_pos_color" | |
| 115 value="blue" | |
| 116 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." /> | |
| 117 <expand macro="jb_color" | |
| 118 label="JBrowse style.neg_color" | |
| 119 name="style_neg_color" | |
| 120 value="red" | |
| 121 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." /> | |
| 122 </expand> | |
| 123 | |
| 124 <conditional name="bicolor_pivot" label="Bicolor Pivot"> | |
| 125 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select"> | |
| 126 <option value="zero" selected="true">Zero</option> | |
| 127 <option value="mean">Mean</option> | |
| 128 <option value="custom">Custom Value</option> | |
| 129 </param> | |
| 130 <when value="zero" /> | |
| 131 <when value="mean" /> | |
| 132 <when value="custom"> | |
| 133 <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." /> | |
| 134 </when> | |
| 135 </conditional> | |
| 136 </section> | |
| 137 </xml> | |
| 138 | |
| 139 <xml name="color_selection" | |
| 140 token_scaling_lin_select="true" | |
| 141 token_scaling_log_select="false" | |
| 142 > | |
| 143 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false"> | |
| 144 <conditional name="color_score" label="JBrowse style.color & Score relationship"> | |
| 145 <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track"> | |
| 146 <option value="score">Based on score</option> | |
| 147 <option value="none" selected="true">Ignore score</option> | |
| 148 </param> | |
| 149 <when value="none"> | |
| 150 <!-- When no scaling is done, no scores available, then just let the | |
| 151 user choose a base color for the track --> | |
| 152 <expand macro="auto_color" /> | |
| 153 </when> | |
| 154 <when value="score"> | |
| 155 <!-- Scaling --> | |
| 156 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" | |
| 157 help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution."> | |
| 158 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option> | |
| 159 <option value="logarithmic" selected="" >Logarithmic scaling</option> | |
| 160 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option> | |
| 161 </param> | |
| 162 | |
| 163 <!-- Scaling Bounds --> | |
| 164 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> | |
| 165 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select"> | |
| 166 <option value="automatic" selected="true">Automatically determined</option> | |
| 167 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> | |
| 168 </param> | |
| 169 <when value="automatic"> | |
| 170 </when> | |
| 171 <when value="manual"> | |
| 172 <param label="Minimum expected score" name="minimum" type="integer" value="0" /> | |
| 173 <param label="Maximum expected score" name="maximum" type="integer" value="100" /> | |
| 174 </when> | |
| 175 </conditional> | |
| 176 | |
| 177 <!-- Scale color --> | |
| 178 <conditional name="color_scheme" label="Color Scheme for scored features"> | |
| 179 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme"> | |
| 180 <option value="opacity">Opacity (high scores = 1.0 opacity)</option> | |
| 181 <!--<option value="brewer">Brewer Color Schemes</option>--> | |
| 182 </param> | |
| 183 <when value="opacity"> | |
| 184 <!-- Single color selection mode --> | |
| 185 <expand macro="auto_color" /> | |
| 186 </when> | |
| 187 <!--<when value="brewer">--> | |
| 188 <!--[> Brewer continuum selection <]--> | |
| 189 <!--<expand macro="brewer_scheme" />--> | |
| 190 <!--</when>--> | |
| 191 </conditional> | |
| 192 </when> | |
| 193 </conditional> | |
| 194 </section> | |
| 195 </xml> | |
| 196 <xml name="track_styling" | |
| 197 token_classname="feature" | |
| 198 token_label="name,id" | |
| 199 token_description="note,description" | |
| 200 token_height="100px"> | |
| 201 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> | |
| 202 <param label="JBrowse style.className" type="text" | |
| 203 name="style_classname" | |
| 204 value="@CLASSNAME@" | |
| 205 help="Set CSS style.className property"/> | |
| 206 <param label="JBrowse style.label" | |
| 207 type="text" | |
| 208 name="style_label" | |
| 209 value="@LABEL@" | |
| 210 help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" /> | |
| 211 <param label="JBrowse style.description" | |
| 212 type="text" | |
| 213 name="style_description" | |
| 214 value="@DESCRIPTION@" | |
| 215 help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/> | |
| 216 <param label="JBrowse style.height" | |
| 217 type="text" | |
| 218 name="style_height" | |
| 219 value="@HEIGHT@" | |
| 220 help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/> | |
| 221 </section> | |
| 222 </xml> | |
| 223 | |
| 224 <xml name="input_conditional" token_label="Track Data" token_format="data"> | |
| 225 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/> | |
| 226 </xml> | |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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227 </macros> |