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comparison nanoplot.xml @ 5:a3c4fe6f49ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
author iuc
date Thu, 16 Jun 2022 20:08:15 +0000
parents edbb6c5028f5
children 0f1c34698076
comparison
equal deleted inserted replaced
4:edbb6c5028f5 5:a3c4fe6f49ab
1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1" profile="20.05">
2 <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description> 2 <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.28.2</token> 4 <token name="@TOOL_VERSION@">1.36.2</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
8 </requirements> 8 </requirements>
9 <stdio>
10 <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem" />
11 </stdio>
9 <version_command>NanoPlot --version</version_command> 12 <version_command>NanoPlot --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 ## set TMPDIR if not already set by admin
15 ## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0`
16 ## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR};
17
11 #set $myfiles = $mode.reads.files 18 #set $myfiles = $mode.reads.files
12
13 #set reads_temp = [] 19 #set reads_temp = []
14 #if $mode.choice == 'combined': 20 #if $mode.choice == 'combined':
15 #for $i, $f in enumerate($myfiles) 21 #for $i, $f in enumerate($myfiles)
16 #if $f.ext == "fastqsanger": 22 #if $f.ext.startswith("fastq"):
17 #set $extension = 'fastq' 23 #set $extension = 'fastq'
18 #else 24 #else
19 #set $extension = $f.ext 25 #set $extension = $f.ext
20 #end if 26 #end if
27 #if $f.ext.endswith(".gz"):
28 #set $f = $extension + ".gz"
29 #else if $f.ext.endswith(".bz"):
30 #set $extension = $extension + "bz2"
31 #end if
21 ln -s '$f' './read_${i}.$extension' && 32 ln -s '$f' './read_${i}.$extension' &&
33 #if "bam" in $extension
34 ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' &&
35 #end if
22 $reads_temp.append("read_" + str($i) + "." + str($extension)) 36 $reads_temp.append("read_" + str($i) + "." + str($extension))
23 #end for 37 #end for
24 #else 38 #else
25 #if $myfiles.ext == "fastqsanger": 39 #if $myfiles.ext.startswith("fastq"):
26 #set $extension = 'fastq' 40 #set $extension = 'fastq'
27 #else 41 #else
28 #set $extension = $myfiles.ext 42 #set $extension = $myfiles.ext
29 #end if 43 #end if
30 ln -s '$mode.reads.files' './read.$extension' && 44 #if $myfiles.ext.endswith(".gz"):
45 #set $extension = $extension + ".gz"
46 #else if $myfiles.ext.endswith(".bz"):
47 #set $extension = $extension + "bz2"
48 #end if
49 ln -s '$myfiles' './read.$extension' &&
50 #if "bam" in $extension
51 ln -s '$myfiles.metadata.bam_index' './read.${extension}.bai' &&
52 #end if
31 $reads_temp.append("read." + str($extension)) 53 $reads_temp.append("read." + str($extension))
32 #end if 54 #end if
33 55
34 NanoPlot 56 NanoPlot
35 --threads \${GALAXY_SLOTS:-4} 57 --threads \${GALAXY_SLOTS:-4}
58 --tsv_stats
36 --$mode.reads.type ${' '.join($reads_temp)} 59 --$mode.reads.type ${' '.join($reads_temp)}
37 #if $filter.maxlength 60 #if $filter.maxlength
38 --maxlength $filter.maxlength 61 --maxlength $filter.maxlength
39 #end if 62 #end if
40 #if $filter.minlength 63 #if $filter.minlength
44 --downsample $filter.downsample 67 --downsample $filter.downsample
45 #end if 68 #end if
46 #if $filter.minqual 69 #if $filter.minqual
47 --minqual $filter.minqual 70 --minqual $filter.minqual
48 #end if 71 #end if
72 #if $filter.runtime_until
73 -- $filter.runtime_until
74 #end if
49 #if $filter.readtype 75 #if $filter.readtype
50 --readtype $filter.readtype 76 --readtype $filter.readtype
51 #end if 77 #end if
52 #if $customization.color 78 #if $customization.color
53 --color $customization.color 79 --color $customization.color
54 #end if
55 #if $customization.format
56 --format $customization.format
57 #end if 80 #end if
58 #if $customization.plots 81 #if $customization.plots
59 --plots ${str($customization.plots).replace(',', ' ')} 82 --plots ${str($customization.plots).replace(',', ' ')}
60 #end if 83 #end if
61 $filter.drop_outliers 84 $filter.drop_outliers
62 $filter.loglength 85 $filter.loglength
63 $filter.percentqual 86 $filter.percentqual
64 $filter.alength 87 $filter.alength
65 $filter.barcoded 88 $filter.barcoded
89 $filter.no_supplementary
66 $customization.N50 90 $customization.N50
67 -o '.' 91 -o '.'
92 && >&2 cat *log
68 ]]></command> 93 ]]></command>
69 <inputs> 94 <inputs>
70 <conditional name="mode"> 95 <conditional name="mode">
71 <param name="choice" type="select" label="Select multifile mode" help="When supplying multiple files, batch mode will run NanoPlot on each file separately, while combined mode will run NanoPlot once on all the reads together. When only supplying a single input file, this setting does not matter."> 96 <param name="choice" type="select" label="Select multifile mode" help="When supplying multiple files, batch mode will run NanoPlot on each file separately, while combined mode will run NanoPlot once on all the reads together. When only supplying a single input file, this setting does not matter.">
72 <option value="batch" selected="true">batch</option> 97 <option value="batch" selected="true">batch</option>
188 type="integer" 213 type="integer"
189 argument="--minqual" 214 argument="--minqual"
190 optional="true" 215 optional="true"
191 label="Drop reads with an average quality lower than specified."/> 216 label="Drop reads with an average quality lower than specified."/>
192 <param 217 <param
218 type="integer"
219 argument="--runtime_until"
220 optional="true"
221 label="Only take the N first hours of a run"/>
222 <param
193 type="select" 223 type="select"
194 argument="--readtype" 224 argument="--readtype"
195 optional="true" 225 optional="true"
196 label="Which read type to extract information about from summary."> 226 label="Which read type to extract information about from summary.">
197 <option value="1D">1D</option> 227 <option value="1D">1D</option>
202 type="boolean" 232 type="boolean"
203 argument="--barcoded" 233 argument="--barcoded"
204 truevalue="--barcoded" 234 truevalue="--barcoded"
205 falsevalue="" 235 falsevalue=""
206 label="Use if you want to split the summary file by barcode."/> 236 label="Use if you want to split the summary file by barcode."/>
237 <param
238 type="boolean"
239 argument="--no_supplementary"
240 truevalue="--no_supplementary"
241 falsevalue=""
242 label="Use if you want to remove supplementary alignments"/>
207 </section> 243 </section>
208 <section 244 <section
209 name="customization" 245 name="customization"
210 title="Options for customizing the plots created" 246 title="Options for customizing the plots created"
211 expanded="false"> 247 expanded="false">
363 <option value="yellowgreen">yellowgreen</option> 399 <option value="yellowgreen">yellowgreen</option>
364 <option value="yellow">yellow</option> 400 <option value="yellow">yellow</option>
365 </param> 401 </param>
366 <param 402 <param
367 type="select" 403 type="select"
368 argument="--format"
369 optional="true"
370 label="Specify the output format of the plots.">
371 <option selected="True" value="png">png</option>
372 <option value="svg">svg</option>
373 </param>
374 <param
375 type="select"
376 argument="--plots" 404 argument="--plots"
377 optional="true" 405 optional="true"
378 multiple="true" 406 multiple="true"
379 display="checkboxes" 407 display="checkboxes"
380 label="Specify the bivariate format of the plots."> 408 label="Specify the bivariate format of the plots.">
381 <option value="kde">kde</option> 409 <option value="kde">kernel density estimation (kde)</option>
382 <option value="hex">hex</option> 410 <option value="dot">dots (dot)</option>
383 <option value="dot">dot</option>
384 <option value="pauvre">pauvre</option>
385 </param> 411 </param>
386 <param 412 <param
387 type="boolean" 413 type="boolean"
388 argument="--N50" 414 argument="--N50"
389 truevalue="--N50" 415 truevalue="--N50"
391 label="Show the N50 mark in the read length histogram."/> 417 label="Show the N50 mark in the read length histogram."/>
392 </section> 418 </section>
393 </inputs> 419 </inputs>
394 <outputs> 420 <outputs>
395 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/> 421 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
396 <data name="nanostats" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/> 422 <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
397 <data name="nanostats_post_filtering" format="txt" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/> 423 <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering" />
398 <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length "> 424 <data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
399 <change_format> 425 <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/>
400 <when input="customization.format" value="svg" format="svg"/>
401 </change_format>
402 </data>
403 <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length ">
404 <change_format>
405 <when input="customization.format" value="svg" format="svg"/>
406 </change_format>
407 </data>
408 </outputs> 426 </outputs>
409 <tests> 427 <tests>
410 <test> 428 <test>
411 <conditional name="mode"> 429 <conditional name="mode">
412 <param name="choice" value="batch"/> 430 <param name="choice" value="batch"/>
413 <conditional name="reads"> 431 <conditional name="reads">
414 <param name="type" value="fastq_rich"/> 432 <param name="type" value="fastq_rich"/>
415 <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/> 433 <param name="files" value="reads.fastq.gz" ftype="fastqsanger.gz"/>
416 </conditional> 434 </conditional>
417 </conditional> 435 </conditional>
418 <section name="filter"> 436 <section name="filter">
419 <param name="downsample" value="800"/> 437 <param name="downsample" value="800"/>
420 </section> 438 </section>
421 <section name="customization"> 439 <section name="customization">
422 <param name="plots" value="hex,kde"/> 440 <param name="plots" value="kde"/>
423 </section> 441 </section>
424 <output name="output_html" file="NanoPlot-report.html" ftype="html" lines_diff="8" /> 442 <output name="output_html" ftype="html">
425 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/> 443 <assert_contents>
426 <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/> 444 <has_text text="html"/>
445 <has_text text="mean_qual"/>
446 </assert_contents>
447 </output>
448 <output name="nanostats" file="NanoStats.txt" ftype="tabular"/>
449 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/>
450 <output name="read_length" ftype="png" file="HistogramReadlength.png" compare="sim_size">
451 </output>
452 <output name="log_read_length" ftype="png">
453 <assert_contents>
454 <has_text text="PNG"/>
455 </assert_contents>
456 </output>
427 </test> 457 </test>
428 <test> 458 <test>
429 <conditional name="mode"> 459 <conditional name="mode">
430 <param name="choice" value="combined"/> 460 <param name="choice" value="combined"/>
431 <conditional name="reads"> 461 <conditional name="reads">
437 <param name="maxlength" value="2000"/> 467 <param name="maxlength" value="2000"/>
438 <param name="minlenght" value="1000"/> 468 <param name="minlenght" value="1000"/>
439 </section> 469 </section>
440 <section name="customization"> 470 <section name="customization">
441 <param name="color" value="yellow"/> 471 <param name="color" value="yellow"/>
442 <param name="format" value="svg"/>
443 </section> 472 </section>
444 <output name="output_html" file="bam-report.html" ftype="html" lines_diff="16"> 473 <output name="output_html" ftype="html">
445 <assert_contents> 474 <assert_contents>
446 <has_text text="html"/> 475 <has_text text="html"/>
447 <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific --> 476 <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
448 </assert_contents> 477 </assert_contents>
449 </output> 478 </output>
450 <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/> 479 <output name="read_length" ftype="png">
480 <assert_contents>
481 <has_text text="PNG"/>
482 </assert_contents>
483 </output>
451 </test> 484 </test>
452 <test><!-- test with multiple input files --> 485 <test><!-- test with multiple input files -->
453 <conditional name="mode"> 486 <conditional name="mode">
454 <param name="choice" value="combined"/> 487 <param name="choice" value="combined"/>
455 <conditional name="reads"> 488 <conditional name="reads">
458 </conditional> 491 </conditional>
459 </conditional> 492 </conditional>
460 <output name="output_html" ftype="html"> 493 <output name="output_html" ftype="html">
461 <assert_contents> 494 <assert_contents>
462 <has_text text="html"/> 495 <has_text text="html"/>
463 <not_has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific --> 496 <not_has_text text="Aligned read length vs Percent identity plot using dots"/>
464 <has_text text="&lt;td&gt;9.0&lt;/td&gt;"/> <!--check both files were used 4+5 reads --> 497 <has_text text="&lt;td&gt;9&lt;/td&gt;"/> <!--check both files were used 4+5 reads -->
465 </assert_contents> 498 </assert_contents>
466 </output> 499 </output>
467 </test> 500 </test>
468 </tests> 501 </tests>
469 <help> 502 <help>