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comparison pretext_snapshot.xml @ 0:02b21260faf4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe"
author iuc
date Mon, 05 Apr 2021 17:27:18 +0000
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children 44c66e8d21e6
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-1:000000000000 0:02b21260faf4
1 <tool id="pretext_snapshot" name="Pretext Snapshot" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
2 <macros>
3 <token name="@WRAPPER_VERSION@">0.0.3</token>
4 <token name="@VERSION_SUFFIX@">galaxy0</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@WRAPPER_VERSION@">pretextsnapshot</requirement>
8 <requirement type="package" version="1.601">rename</requirement>
9 </requirements>
10 <version_command>PretextSnapshot --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 PretextSnapshot -m $input
13 -f $formats.outformat
14 #if $formats.outformat == 'jpeg':
15 --jpegQuality $formats.jpegQuality
16 #end if
17 -r $resolution
18 -c $colormap
19 --sequences '$sequences'
20 --minTexels $mintexels
21 #if $grid.showGrid == 'yes':
22 --gridSize $grid.gridsize
23 --gridColour $grid.gridcolor
24 #else:
25 --gridSize 0
26 #end if
27 '${sequencenames}'
28 -o output
29 --prefix pretext_snapshot
30 #if $formats.outformat == 'jpeg':
31 && find ./output/* | rename -s .jpeg .jpg
32 #end if
33 ]]></command>
34 <inputs>
35 <param name="input" type="data" argument="--map" format="pretext" label="Input Pretext map file"/>
36 <conditional name="formats">
37 <param name="outformat" argument="-f" type="select" label="Output image format" help="Format of output image">
38 <option value="png" selected="true"/>
39 <option value="bmp"/>
40 <option value="jpeg"/>
41 </param>
42 <when value="png"/>
43 <when value="bmp"/>
44 <when value="jpeg">
45 <param name="jpegQuality" argument="--jpegQuality" type="integer" label="JPEG quality factor" value="80" min="0" max="100" help="An integer between 1 and 100, default 80. Larger values result in increased image quality and file size."/>
46 </when>
47 </conditional>
48 <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."/>
49 <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"/>
50 <param name="sequences" 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.">
51 <sanitizer invalid_char="">
52 <valid initial="string.ascii_letters,string.digits">
53 <add value="="/>
54 <add value="_"/>
55 <add value="&#32;"/>
56 <add value="&#44;"/>
57 <add value="&#91;"/>
58 <add value="&#93;"/>
59 <add value="&#123;"/>
60 <add value="&#125;"/>
61 <add value="&#35;"/>
62 <add value="&#60;"/>
63 <add value="&#62;"/>
64 </valid>
65 </sanitizer>
66 </param>
67 <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."/>
68 <conditional name="grid">
69 <param name="showGrid" label="Show grid?" type="boolean" truevalue="yes" falsevalue="no"/>
70 <when value="yes">
71 <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."/>
72 <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)."/>
73 </when>
74 <when value="no"/>
75 </conditional>
76 <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."/>
77 </inputs>
78 <outputs>
79 <collection name="pretext_snap_out" type="list" label="${tool.name} on ${on_string}">
80 <discover_datasets directory="output" pattern="__name_and_ext__" />
81 </collection>
82 </outputs>
83 <tests>
84 <test expect_num_outputs="1">
85 <param name="input" value="map.pretext"/>
86 <conditional name="formats">
87 <param name="outformat" value="jpeg"/>
88 <param name="jpegquality" value="80"/>
89 </conditional>
90 <param name="resolution" value="900"/>
91 <param name="colormap" value="1"/>
92 <param name="sequences" value="=full, =all"/>
93 <param name="mintexels" value="30"/>
94 <conditional name="grid">
95 <param name="showGrid" value="yes"/>
96 <param name="gridsize" value="2"/>
97 <param name="gridcolor" value="red"/>
98 </conditional>
99 <param name="sequencenames" value="--printSequenceNames"/>
100 <output_collection name="pretext_snap_out" count="4">
101 <element name="pretext_snapshotFullMap" ftype="jpg" file="fullmap1.jpg"/>
102 <element name="pretext_snapshotref_0" ftype="jpg" file="snapshot1.jpg"/>
103 <element name="pretext_snapshotref_1" ftype="jpg" file="snapshot2.jpg"/>
104 <element name="pretext_snapshotref_2" ftype="jpg" file="snapshot3.jpg"/>
105 </output_collection>
106 </test>
107 <test expect_num_outputs="1">
108 <param name="input" value="map.pretext"/>
109 <conditional name="formats">
110 <param name="outformat" value="bmp"/>
111 </conditional>
112 <param name="resolution" value="700"/>
113 <param name="colormap" value="5"/>
114 <param name="sequences" value="=full"/>
115 <param name="mintexels" value="60"/>
116 <output_collection name="pretext_snap_out" count="1">
117 <element name="pretext_snapshotFullMap" ftype="bmp" file="fullmap2.bmp"/>
118 </output_collection>
119 </test>
120 </tests>
121 <help><![CDATA[
122 **Color map:**
123
124 +---------------------------------------+-------------------------------+-------------------------------+
125 |0. Inferno |11. Blue 4 |22. Orange 2 |
126 +---------------------------------------+-------------------------------+-------------------------------+
127 |1. Black Body |12. Blue-Orange Divergent |23. Orange-Green-Blue-Gray |
128 +---------------------------------------+-------------------------------+-------------------------------+
129 |2. Kindlmann |13. Brown 1 |24. Purple 1 |
130 +---------------------------------------+-------------------------------+-------------------------------+
131 |3. Extended Kindlmann |14. Brown 2 |25. Purple 2 |
132 +---------------------------------------+-------------------------------+-------------------------------+
133 |4. Three Wave Yellow-Grey-Blue |15. Brown 3 |26. Red 1 |
134 +---------------------------------------+-------------------------------+-------------------------------+
135 |5. Three Wave Blue-Green-Yellow |16. Green 1 |27. Red 2 |
136 +---------------------------------------+-------------------------------+-------------------------------+
137 |6. Four Wave Grey-Red-Green |17. Green 2 |28. Red 3 |
138 +---------------------------------------+-------------------------------+-------------------------------+
139 |7. Five Wave Yellow-Brown-Blue |18. Green 3 |29. Yellow 1 |
140 +---------------------------------------+-------------------------------+-------------------------------+
141 |8. Blue 1 |19. Green 4 |30. Yellow 2 |
142 +---------------------------------------+-------------------------------+-------------------------------+
143 |9. Blue 2 |20. Mellow Rainbow | |
144 +---------------------------------------+-------------------------------+-------------------------------+
145 |10. Blue 3 |21. Orange 1 | |
146 +---------------------------------------+-------------------------------+-------------------------------+
147
148
149 **Sequence strings:**
150
151 * --sequences "=full"
152
153 * Creates a single image of the full contact map.
154
155 * --sequences "=full, =all"
156
157 * Creates an image of the full contact map, plus an image of each sequence.
158
159 * --sequences "seq_0"
160
161 * Creates a single image of the sequence named "seq_0"
162
163 * --sequences "seq_0, seq_1 > seq_2"
164
165 * Creates an image of seq_0, and an image from the start of seq_1 to the end of seq_2
166
167 * --sequences "seq_0[1000000] > seq_3"
168
169 * Creates an image starting 1Mbp into seq_0, ending at the end of seq_3
170
171 * --sequences "{seq_0, seq_1}"
172
173 * Create an single image of the off-diagonal region between seq_0 and seq_1,
174 * i.e. the inter-sequence map of seq_0 and seq_1.
175
176 * --sequences "{seq_2[2000000] > seq_4[1000000] , seq_0[3000000] > seq_1[4000000]} , seq_0 > seq_10"
177
178 * 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.
179 * The second image is the diagonal region between the start of seq_0 and the end of seq_10.
180
181 ]]></help>
182 <citations>
183 <citation type="bibtex">
184 @misc{Harry_et_al,
185 Author={Harry, E},
186 title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
187 url = {https://github.com/wtsi-hpag/PretextSnapshot},}
188 </citation>
189 </citations>
190 </tool>