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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
author iuc
date Fri, 28 Sep 2018 19:30:29 -0400
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1 <tool id="nanoplot" name="NanoPlot" version="1.13.0">
2 <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
3 <requirements>
4 <requirement type="package" version="1.18.2">nanoplot</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8
9 #set reads_temp = []
10 #for $i, $f in enumerate($reads.files)
11 #set $extension = $f.ext
12 #if $extension == 'fastqsanger'
13 #set $extension = 'fastq'
14 #end if
15 ln -s '$f' './read_${i}.$extension' &&
16 $reads_temp.append("read_" + str($i) + "." + str($extension))
17 #end for
18
19 NanoPlot
20 --$reads.type ${' '.join($reads_temp)}
21
22 #if $filter.maxlength
23 --maxlength $filter.maxlength
24 #end if
25 #if $filter.minlength
26 --minlength $filter.minlength
27 #end if
28 #if $filter.downsample
29 --downsample $filter.downsample
30 #end if
31 #if $filter.minqual
32 --minqual $filter.minqual
33 #end if
34 #if $filter.readtype
35 --readtype $filter.readtype
36 #end if
37 #if $customization.color
38 --color $customization.color
39 #end if
40 #if $customization.format
41 --format $customization.format
42 #end if
43 #if $customization.plots
44 --plots ${str($customization.plots).replace(',', ' ')}
45 #end if
46 $filter.drop_outliers
47 $filter.loglength
48 $filter.percentqual
49 $filter.alength
50 $filter.barcoded
51 $customization.noN50
52 $customization.N50
53 -o '.'
54 ]]>
55 </command>
56 <inputs>
57 <conditional name="reads">
58 <param name="type" type="select" label="Type of the file(s) to work on">
59 <option value="fastq" selected="true">fastq</option>
60 <option value="fasta">fasta</option>
61 <option value="fastq_rich">fastq_rich</option>
62 <option value="fastq_minimal">fastq_minimal</option>
63 <option value="summary">summary</option>
64 <option value="bam">bam</option>
65 <option value="cram">cram</option>
66 </param>
67 <when value="fastq">
68 <param
69 type="data"
70 argument="--fastq"
71 name="files"
72 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"
73 multiple="true"/>
74 </when>
75 <when value="fasta">
76 <param
77 type="data"
78 argument="--fasta"
79 name="files"
80 format="fasta,fasta.gz,vcf_bgzip"
81 multiple="true"/>
82 </when>
83 <when value="fastq_rich">
84 <param
85 type="data"
86 argument="--fastq_rich"
87 name="files"
88 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"
89 multiple="true"/>
90 </when>
91 <when value="fastq_minimal">
92 <param
93 type="data"
94 argument="--fastq_minimal"
95 name="files"
96 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"
97 multiple="true"/>
98 </when>
99 <when value="summary">
100 <param
101 type="data"
102 argument="--summary"
103 name="files"
104 format="txt,zip"
105 multiple="true"/>
106 </when>
107 <when value="bam">
108 <param
109 type="data"
110 argument="--bam"
111 name="files"
112 format="bam"
113 multiple="true"/>
114 </when>
115 <when value="cram">
116 <param
117 type="data"
118 argument="--cram"
119 name="files"
120 format="cram"
121 multiple="true"/>
122 </when>
123 </conditional>
124 <section
125 name="filter"
126 title="Options for filtering or transforming input prior to plotting"
127 expanded="false">
128 <param
129 type="integer"
130 argument="--maxlength"
131 optional="true"
132 label="Drop reads longer than length specified."/>
133 <param
134 type="integer"
135 argument="--minlength"
136 optional="true"
137 label="Drop reads shorter than length specified."/>
138 <param
139 type="boolean"
140 argument="--drop_outliers"
141 truevalue="--drop_outliers"
142 falsevalue=""
143 label="Drop outlier reads with extreme long length."/>
144 <param
145 type="integer"
146 argument="--downsample"
147 optional="true"
148 label="Reduce dataset to N reads by random sampling."/>
149 <param
150 type="boolean"
151 argument="--loglength"
152 truevalue="--loglength"
153 falsevalue=""
154 label="Logarithmic scaling of lengths in plots."/>
155 <param
156 type="boolean"
157 argument="--percentqual"
158 truevalue="--percentqual"
159 falsevalue=""
160 label="Use qualities as theoretical percent identities."/>
161 <param
162 type="boolean"
163 argument="--alength"
164 truevalue="--alength"
165 falsevalue=""
166 label="Use aligned read lengths rather than sequenced length (bam mode)."/>
167 <param
168 type="integer"
169 argument="--minqual"
170 optional="true"
171 label="Drop reads with an average quality lower than specified."/>
172 <param
173 type="select"
174 argument="--readtype"
175 optional="true"
176 label="Which read type to extract information about from summary.">
177 <option value="1D">1D</option>
178 <option value="2D">2D</option>
179 <option value="1D2">1D2</option>
180 </param>
181 <param
182 type="boolean"
183 argument="--barcoded"
184 truevalue="--barcoded"
185 falsevalue=""
186 label="Use if you want to split the summary file by barcode."/>
187 </section>
188 <section
189 name="customization"
190 title="Options for customizing the plots created"
191 expanded="false">
192 <param
193 type="select"
194 argument="--color"
195 optional="true"
196 label="Specify a color for the plots.">
197 <option value="aliceblue">aliceblue</option>
198 <option value="antiquewhite">antiquewhite</option>
199 <option value="aqua">aqua</option>
200 <option value="aquamarine">aquamarine</option>
201 <option value="azure">azure</option>
202 <option value="beige">beige</option>
203 <option value="bisque">bisque</option>
204 <option value="black">black</option>
205 <option value="blanchedalmond">blanchedalmond</option>
206 <option value="blue">blue</option>
207 <option value="blueviolet">blueviolet</option>
208 <option value="brown">brown</option>
209 <option value="burlywood">burlywood</option>
210 <option value="cadetblue">cadetblue</option>
211 <option value="chartreuse">chartreuse</option>
212 <option value="chocolate">chocolate</option>
213 <option value="coral">coral</option>
214 <option value="cornflowerblue">cornflowerblue</option>
215 <option value="cornsilk">cornsilk</option>
216 <option value="crimson">crimson</option>
217 <option value="cyan">cyan</option>
218 <option value="darkblue">darkblue</option>
219 <option value="darkcyan">darkcyan</option>
220 <option value="darkgoldenrod">darkgoldenrod</option>
221 <option value="darkgray">darkgray</option>
222 <option value="darkgreen">darkgreen</option>
223 <option value="darkgrey">darkgrey</option>
224 <option value="darkkhaki">darkkhaki</option>
225 <option value="darkmagenta">darkmagenta</option>
226 <option value="darkolivegreen">darkolivegreen</option>
227 <option value="darkorange">darkorange</option>
228 <option value="darkorchid">darkorchid</option>
229 <option value="darkred">darkred</option>
230 <option value="darksalmon">darksalmon</option>
231 <option value="darkseagreen">darkseagreen</option>
232 <option value="darkslateblue">darkslateblue</option>
233 <option value="darkslategray">darkslategray</option>
234 <option value="darkslategrey">darkslategrey</option>
235 <option value="darkturquoise">darkturquoise</option>
236 <option value="darkviolet">darkviolet</option>
237 <option value="deeppink">deeppink</option>
238 <option value="deepskyblue">deepskyblue</option>
239 <option value="dimgray">dimgray</option>
240 <option value="dimgrey">dimgrey</option>
241 <option value="dodgerblue">dodgerblue</option>
242 <option value="firebrick">firebrick</option>
243 <option value="floralwhite">floralwhite</option>
244 <option value="forestgreen">forestgreen</option>
245 <option value="fuchsia">fuchsia</option>
246 <option value="gainsboro">gainsboro</option>
247 <option value="ghostwhite">ghostwhite</option>
248 <option value="goldenrod">goldenrod</option>
249 <option value="gold">gold</option>
250 <option value="gray">gray</option>
251 <option value="green">green</option>
252 <option value="greenyellow">greenyellow</option>
253 <option value="grey">grey</option>
254 <option value="honeydew">honeydew</option>
255 <option value="hotpink">hotpink</option>
256 <option value="indianred">indianred</option>
257 <option value="indigo">indigo</option>
258 <option value="ivory">ivory</option>
259 <option value="khaki">khaki</option>
260 <option value="lavenderblush">lavenderblush</option>
261 <option value="lavender">lavender</option>
262 <option value="lawngreen">lawngreen</option>
263 <option value="lemonchiffon">lemonchiffon</option>
264 <option value="lightblue">lightblue</option>
265 <option value="lightcoral">lightcoral</option>
266 <option value="lightcyan">lightcyan</option>
267 <option value="lightgoldenrodyellow">lightgoldenrodyellow</option>
268 <option value="lightgray">lightgray</option>
269 <option value="lightgreen">lightgreen</option>
270 <option value="lightgrey">lightgrey</option>
271 <option value="lightpink">lightpink</option>
272 <option value="lightsalmon">lightsalmon</option>
273 <option value="lightseagreen">lightseagreen</option>
274 <option value="lightskyblue">lightskyblue</option>
275 <option value="lightslategray">lightslategray</option>
276 <option value="lightslategrey">lightslategrey</option>
277 <option value="lightsteelblue">lightsteelblue</option>
278 <option value="lightyellow">lightyellow</option>
279 <option value="limegreen">limegreen</option>
280 <option value="lime">lime</option>
281 <option value="linen">linen</option>
282 <option value="magenta">magenta</option>
283 <option value="maroon">maroon</option>
284 <option value="mediumaquamarine">mediumaquamarine</option>
285 <option value="mediumblue">mediumblue</option>
286 <option value="mediumorchid">mediumorchid</option>
287 <option value="mediumpurple">mediumpurple</option>
288 <option value="mediumseagreen">mediumseagreen</option>
289 <option value="mediumslateblue">mediumslateblue</option>
290 <option value="mediumspringgreen">mediumspringgreen</option>
291 <option value="mediumturquoise">mediumturquoise</option>
292 <option value="mediumvioletred">mediumvioletred</option>
293 <option value="midnightblue">midnightblue</option>
294 <option value="mintcream">mintcream</option>
295 <option value="mistyrose">mistyrose</option>
296 <option value="moccasin">moccasin</option>
297 <option value="navajowhite">navajowhite</option>
298 <option value="navy">navy</option>
299 <option value="oldlace">oldlace</option>
300 <option value="olivedrab">olivedrab</option>
301 <option value="olive">olive</option>
302 <option value="orange">orange</option>
303 <option value="orangered">orangered</option>
304 <option value="orchid">orchid</option>
305 <option value="palegoldenrod">palegoldenrod</option>
306 <option value="palegreen">palegreen</option>
307 <option value="paleturquoise">paleturquoise</option>
308 <option value="palevioletred">palevioletred</option>
309 <option value="papayawhip">papayawhip</option>
310 <option value="peachpuff">peachpuff</option>
311 <option value="peru">peru</option>
312 <option value="pink">pink</option>
313 <option value="plum">plum</option>
314 <option value="powderblue">powderblue</option>
315 <option value="purple">purple</option>
316 <option value="rebeccapurple">rebeccapurple</option>
317 <option value="red">red</option>
318 <option value="rosybrown">rosybrown</option>
319 <option value="royalblue">royalblue</option>
320 <option value="saddlebrown">saddlebrown</option>
321 <option value="salmon">salmon</option>
322 <option value="sandybrown">sandybrown</option>
323 <option value="seagreen">seagreen</option>
324 <option value="seashell">seashell</option>
325 <option value="sienna">sienna</option>
326 <option value="silver">silver</option>
327 <option value="skyblue">skyblue</option>
328 <option value="slateblue">slateblue</option>
329 <option value="slategray">slategray</option>
330 <option value="slategrey">slategrey</option>
331 <option value="snow">snow</option>
332 <option value="springgreen">springgreen</option>
333 <option value="steelblue">steelblue</option>
334 <option value="tan">tan</option>
335 <option value="teal">teal</option>
336 <option value="thistle">thistle</option>
337 <option value="tomato">tomato</option>
338 <option value="turquoise">turquoise</option>
339 <option value="violet">violet</option>
340 <option value="wheat">wheat</option>
341 <option value="whitesmoke">whitesmoke</option>
342 <option value="white">white</option>
343 <option value="yellowgreen">yellowgreen</option>
344 <option value="yellow">yellow</option>
345 </param>
346 <param
347 type="select"
348 argument="--format"
349 optional="true"
350 label="Specify the output format of the plots.">
351 <option selected="True" value="png">png</option>
352 <option value="jpg">jpg</option>
353 <option value="svg">svg</option>
354 </param>
355 <param
356 type="select"
357 argument="--plots"
358 optional="true"
359 multiple="true"
360 display="checkboxes"
361 label="Specify the bivariate format of the plots.">
362 <option value="kde">kde</option>
363 <option value="hex">hex</option>
364 <option value="dot">dot</option>
365 <option value="pauvre">pauvre</option>
366 </param>
367 <param
368 type="boolean"
369 name="noN50"
370 truevalue="--no-N50"
371 falsevalue=""
372 label="Hide the N50 mark in the read length histogram."/>
373 <param
374 type="boolean"
375 argument="--N50"
376 truevalue="--N50"
377 falsevalue=""
378 label="Show the N50 mark in the read length histogram."/>
379 </section>
380 </inputs>
381 <outputs>
382 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
383 <data name="nanostats" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
384 <data name="nanostats_post_filtering" format="txt" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
385 <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length ">
386 <change_format>
387 <when input="customization.format" value="jpg" format="jpg"/>
388 <when input="customization.format" value="svg" format="svg"/>
389 </change_format>
390 </data>
391 <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length ">
392 <change_format>
393 <when input="customization.format" value="jpg" format="jpg"/>
394 <when input="customization.format" value="svg" format="svg"/>
395 </change_format>
396 </data>
397 </outputs>
398 <tests>
399 <test>
400 <conditional name="reads">
401 <param name="type" value="fastq_rich"/>
402 <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/>
403 </conditional>
404 <section name="filter">
405 <param name="downsample" value="800"/>
406 </section>
407 <section name="customization">
408 <param name="plots" value="hex,kde"/>
409 <param name="title" value="My Plot"/>
410 <param name="format" value="jpg"/>
411 </section>
412 <output name="output_html" file="NanoPlot-report.html" ftype="html"/>
413 <output name="nanostats" file="NanoStats.txt" ftype="txt"/>
414 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>
415 <output name="read_length" file="HistogramReadlength.jpg" ftype="jpg" compare="sim_size" delta="30000"/>
416 </test>
417 <test>
418 <conditional name="reads">
419 <param name="type" value="bam"/>
420 <param name="files" value="alignment.bam" ftype="bam"/>
421 </conditional>
422 <section name="filter">
423 <param name="maxlength" value="2000"/>
424 <param name="minlenght" value="1000"/>
425 </section>
426 <section name="customization">
427 <param name="color" value="yellow"/>
428 <param name="format" value="svg"/>
429 <param name="noN50" value="True"/>
430 </section>
431 <output name="output_html" file="bam-report.html" ftype="html" compare="sim_size" delta="50000"/>
432 <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>
433 </test>
434
435 </tests>
436 <help>
437 <![CDATA[
438
439 **What it does**
440
441 NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_
442
443 .. _NanoPlot: https://github.com/wdecoster/NanoPlot
444 .. _`Wouter De Coster`: https://github.com/wdecoster
445
446 **Input**
447
448 NanoPlot requires 1 or more files as input. They can either be fastq (can be generated
449 by albacore, guppy or MinKNOW containing additional information), fasta, sorted bam,
450 sorted cram or sequencing summary.
451
452 **Output**
453
454 NanoPlot produces different number of plots depending on the data and customizations.
455 A detailed view can be seen on here_. Additionally a file showing the statistics
456 is generated.
457
458 .. _here: https://github.com/wdecoster/NanoPlot#plots-generated
459 ]]>
460 </help>
461 <citations>
462 <citation type="bibtex">
463 @misc{githubnanoplot, author = {De Coster, Wouter}, year = {2018}, title =
464 {NanoPlot}, publisher = {GitHub}, journal = {GitHub repository}, url =
465 {https://github.com/wdecoster/NanoPlot}, }</citation>
466 <citation type="doi">10.1093/bioinformatics/bty149</citation>
467 </citations>
468 </tool>