Mercurial > repos > iuc > pretext_snapshot

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
author iuc
date Fri, 07 Nov 2025 16:39:39 +0000
parents ec1336a26fa1
children
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1 <tool id="pretext_snapshot" name="Pretext Snapshot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>image generator for Pretext contact maps</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.0.5</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">pretextsnapshot</requirement>
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9 <requirement type="package" version="1.601">rename</requirement>
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10 </requirements>
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11 <version_command>PretextSnapshot --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 PretextSnapshot -m $input
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14 -f $formats.outformat
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15 #if $formats.outformat == 'jpeg':
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16 --jpegQuality $formats.jpegQuality
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17 #end if
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18 -r $resolution
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19 -c $colormap
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20 --sequences '$sequences'
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21 --minTexels $mintexels
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22 #if $grid.showGrid == 'yes':
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23 --gridSize $grid.gridsize
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24 --gridColour $grid.gridcolor
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25 #else:
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26 --gridSize 0
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27 #end if
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28 '${sequencenames}'
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29 -o output
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30 --prefix pretext_snapshot
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31 #if $formats.outformat == 'jpeg':
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32 && find ./output/* | rename -s .jpeg .jpg
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33 #end if
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34 ]]></command>
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35 <inputs>
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36 <param name="input" type="data" argument="--map" format="pretext" label="Input Pretext map file"/>
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37 <conditional name="formats">
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38 <param name="outformat" argument="-f" type="select" label="Output image format" help="Format of output image">
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39 <option value="png" selected="true">PNG</option>
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40 <option value="bmp">BMP</option>
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41 <option value="jpeg">JPG</option>
0
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42 </param>
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43 <when value="png"/>
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44 <when value="bmp"/>
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45 <when value="jpeg">
4
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46 <param argument="--jpegQuality" type="integer" label="JPEG quality factor" value="80" min="0" max="100" help="An integer between 0 and 100, default 80. Larger values result in increased image quality and file size."/>
0
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47 </when>
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48 </conditional>
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49 <param name="resolution" argument="-r" type="integer" label="Output image resolution" min="1" value="1000" help="Image resolution, a positive integer, default 1080. For non-square images this will be the resolution of the longest dimension."/>
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50 <param name="colormap" argument='-c' type="integer" label="Color Map" value="5" min="0" max="30" help="Color map based on list available in the help section"/>
4
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51 <param argument="--sequences" type="text" label="Sequence specification string" value="=full, =all" help="Each entry, except for '=all', corresponds to one output image. More information available in the help section.">
0
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52 <sanitizer invalid_char="">
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53 <valid initial="string.ascii_letters,string.digits">
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54 <add value="="/>
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55 <add value="_"/>
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56 <add value="&#32;"/>
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57 <add value="&#44;"/>
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58 <add value="&#91;"/>
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59 <add value="&#93;"/>
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60 <add value="&#123;"/>
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61 <add value="&#125;"/>
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62 <add value="&#35;"/>
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63 <add value="&#60;"/>
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64 <add value="&#62;"/>
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65 </valid>
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66 </sanitizer>
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67 </param>
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68 <param name="mintexels" argument="--minTexels" type="integer" min="1" label="Min Texels" value="64" help="Minimum map texels per image (along a single dimension), a positive integer, Output images over too small a range that violate this minimum will not be created."/>
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69 <conditional name="grid">
4
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70 <param name="showGrid" label="Show grid?" type="select">
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71 <option value="no">No</option>
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72 <option value="yes">Yes</option>
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73 </param>
0
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74 <when value="yes">
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75 <param name="gridsize" argument="--gridSize" type="integer" label="Grid size" value="1" min="1" help="Width in pixels of the sequence separation grid, a non-negative integer. Set to 0 to not overlay a grid."/>
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76 <param name="gridcolor" argument="--gridColour" type="text" label="Grid color" value="black" help="Colour of the sequence separation grid. Either, one of: 'black'(default), 'white', 'red', 'green', 'blue', 'yellow', 'cyan' or 'magenta'. Or, a sRGBA 32-bit hex code in RRGGBBAA format, e.g. 'ff00ff80' (magenta at half-occupancy)."/>
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77 </when>
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78 <when value="no"/>
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79 </conditional>
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80 <param name="sequencenames" argument="--printSequenceNames" type="boolean" label="Print Sequence names" truevalue="--printSequenceNames" falsevalue="" help="Print list of all individual suequeces names on the map, in order of appearance."/>
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81 </inputs>
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82 <outputs>
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83 <collection name="pretext_snap_out" type="list" label="${tool.name} on ${on_string}">
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84 <discover_datasets directory="output" pattern="__name_and_ext__" />
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
85 </collection>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
86 </outputs>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
87 <tests>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
88 <test expect_num_outputs="1">
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
89 <param name="input" value="map.pretext"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
90 <conditional name="formats">
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
91 <param name="outformat" value="jpeg"/>
6
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
92 <param name="jpegQuality" value="80"/>
0
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
93 </conditional>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
94 <param name="resolution" value="900"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
95 <param name="colormap" value="1"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
96 <param name="sequences" value="=full, =all"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
97 <param name="mintexels" value="30"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
98 <conditional name="grid">
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
99 <param name="showGrid" value="yes"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
100 <param name="gridsize" value="2"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
101 <param name="gridcolor" value="red"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
102 </conditional>
6
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
103 <param name="sequencenames" value="True"/>
0
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
104 <output_collection name="pretext_snap_out" count="4">
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
105 <element name="pretext_snapshotFullMap" ftype="jpg" file="fullmap1.jpg"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
106 <element name="pretext_snapshotref_0" ftype="jpg" file="snapshot1.jpg"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
107 <element name="pretext_snapshotref_1" ftype="jpg" file="snapshot2.jpg"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
108 <element name="pretext_snapshotref_2" ftype="jpg" file="snapshot3.jpg"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
109 </output_collection>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
110 </test>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
111 <test expect_num_outputs="1">
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
112 <param name="input" value="map.pretext"/>
6
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
113 <param name="sequencenames" value="True"/>
0
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
114 <conditional name="formats">
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
115 <param name="outformat" value="bmp"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
116 </conditional>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
117 <param name="resolution" value="700"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
118 <param name="colormap" value="5"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
119 <param name="sequences" value="=full"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
120 <param name="mintexels" value="60"/>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
121 <output_collection name="pretext_snap_out" count="1">
6
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
122 <element name="pretext_snapshotFullMap" ftype="bmp">
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
123 <assert_contents>
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
124 <has_size value="1470054" delta="1000"/>
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
125 </assert_contents>
046f51d5f701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext commit f58b497b52f86a3d1c2c5eedbdf684145d43f1e8
iuc
parents: 4
diff changeset
126 </element>
0
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
127 </output_collection>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
128 </test>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
129 </tests>
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
130 <help><![CDATA[
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
131 **Color map:**
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
132
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
133 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
134 |0. Inferno |11. Blue 4 |22. Orange 2 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
135 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
136 |1. Black Body |12. Blue-Orange Divergent |23. Orange-Green-Blue-Gray |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
137 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
138 |2. Kindlmann |13. Brown 1 |24. Purple 1 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
139 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
140 |3. Extended Kindlmann |14. Brown 2 |25. Purple 2 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
141 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
142 |4. Three Wave Yellow-Grey-Blue |15. Brown 3 |26. Red 1 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
143 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
144 |5. Three Wave Blue-Green-Yellow |16. Green 1 |27. Red 2 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
145 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
146 |6. Four Wave Grey-Red-Green |17. Green 2 |28. Red 3 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
147 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
148 |7. Five Wave Yellow-Brown-Blue |18. Green 3 |29. Yellow 1 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
149 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
150 |8. Blue 1 |19. Green 4 |30. Yellow 2 |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
151 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
152 |9. Blue 2 |20. Mellow Rainbow | |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
153 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
154 |10. Blue 3 |21. Orange 1 | |
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
155 +---------------------------------------+-------------------------------+-------------------------------+
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
156
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
157
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
158 **Sequence strings:**
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
159
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
160 * --sequences "=full"
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
161
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
162 * Creates a single image of the full contact map.
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
163
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
164 * --sequences "=full, =all"
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
165
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
166 * Creates an image of the full contact map, plus an image of each sequence.
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
167
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
168 * --sequences "seq_0"
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
169
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
170 * Creates a single image of the sequence named "seq_0"
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
171
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
172 * --sequences "seq_0, seq_1 > seq_2"
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
diff changeset
173
7e3fa7554ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
iuc
parents:
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174 * Creates an image of seq_0, and an image from the start of seq_1 to the end of seq_2
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175
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176 * --sequences "seq_0[1000000] > seq_3"
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177
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178 * Creates an image starting 1Mbp into seq_0, ending at the end of seq_3
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179
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180 * --sequences "{seq_0, seq_1}"
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181
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182 * Create an single image of the off-diagonal region between seq_0 and seq_1,
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183 * i.e. the inter-sequence map of seq_0 and seq_1.
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184
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185 * --sequences "{seq_2[2000000] > seq_4[1000000] , seq_0[3000000] > seq_1[4000000]} , seq_0 > seq_10"
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186
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187 * Creates two images. The first is the off-diagonal region between 2Mbp into seq_2 and 1Mbp into seq_4 along the x-dimension, and 3Mbp into seq_0 and 4Mbp into seq_1 along the y-dimension.
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188 * The second image is the diagonal region between the start of seq_0 and the end of seq_10.
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189
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190 ]]></help>
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191 <citations>
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192 <citation type="bibtex">
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193 @misc{Harry_et_al,
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194 Author={Harry, E},
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195 title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
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196 url = {https://github.com/wtsi-hpag/PretextSnapshot},}
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197 </citation>
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198 </citations>
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199 </tool>