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comparison nanoplot.xml @ 2:acd337269171 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee
author iuc
date Thu, 20 Jun 2019 10:18:48 -0400
parents 4c172a4a4c9e
children 645159bcee2d
comparison
equal deleted inserted replaced
1:4c172a4a4c9e 2:acd337269171
1 <tool id="nanoplot" name="NanoPlot" version="1.13.0"> 1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0">
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>
4 <token name="@TOOL_VERSION@">1.25.0</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.18.2">nanoplot</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
5 </requirements> 8 </requirements>
9 <version_command>NanoPlot --version</version_command>
6 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
7 <![CDATA[ 11 <![CDATA[
8 12
9 #set reads_temp = [] 13 #set reads_temp = []
10 #for $i, $f in enumerate($reads.files) 14 #for $i, $f in enumerate($reads.files)
348 type="select" 352 type="select"
349 argument="--format" 353 argument="--format"
350 optional="true" 354 optional="true"
351 label="Specify the output format of the plots."> 355 label="Specify the output format of the plots.">
352 <option selected="True" value="png">png</option> 356 <option selected="True" value="png">png</option>
353 <option value="jpg">jpg</option>
354 <option value="svg">svg</option> 357 <option value="svg">svg</option>
355 </param> 358 </param>
356 <param 359 <param
357 type="select" 360 type="select"
358 argument="--plots" 361 argument="--plots"
383 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/> 386 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
384 <data name="nanostats" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/> 387 <data name="nanostats" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
385 <data name="nanostats_post_filtering" format="txt" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/> 388 <data name="nanostats_post_filtering" format="txt" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
386 <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length "> 389 <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length ">
387 <change_format> 390 <change_format>
388 <when input="customization.format" value="jpg" format="jpg"/>
389 <when input="customization.format" value="svg" format="svg"/> 391 <when input="customization.format" value="svg" format="svg"/>
390 </change_format> 392 </change_format>
391 </data> 393 </data>
392 <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length "> 394 <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length ">
393 <change_format> 395 <change_format>
394 <when input="customization.format" value="jpg" format="jpg"/>
395 <when input="customization.format" value="svg" format="svg"/> 396 <when input="customization.format" value="svg" format="svg"/>
396 </change_format> 397 </change_format>
397 </data> 398 </data>
398 </outputs> 399 </outputs>
399 <tests> 400 <tests>
406 <param name="downsample" value="800"/> 407 <param name="downsample" value="800"/>
407 </section> 408 </section>
408 <section name="customization"> 409 <section name="customization">
409 <param name="plots" value="hex,kde"/> 410 <param name="plots" value="hex,kde"/>
410 <param name="title" value="My Plot"/> 411 <param name="title" value="My Plot"/>
411 <param name="format" value="jpg"/>
412 </section> 412 </section>
413 <output name="output_html" file="NanoPlot-report.html" ftype="html"/> 413 <output name="output_html" file="NanoPlot-report.html" ftype="html"/>
414 <output name="nanostats" file="NanoStats.txt" ftype="txt"/>
415 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/> 414 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>
416 <output name="read_length" file="HistogramReadlength.jpg" ftype="jpg" compare="sim_size" delta="30000"/> 415 <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/>
417 </test> 416 </test>
418 <test> 417 <test>
419 <conditional name="reads"> 418 <conditional name="reads">
420 <param name="type" value="bam"/> 419 <param name="type" value="bam"/>
421 <param name="files" value="alignment.bam" ftype="bam"/> 420 <param name="files" value="alignment.bam" ftype="bam"/>
427 <section name="customization"> 426 <section name="customization">
428 <param name="color" value="yellow"/> 427 <param name="color" value="yellow"/>
429 <param name="format" value="svg"/> 428 <param name="format" value="svg"/>
430 <param name="noN50" value="True"/> 429 <param name="noN50" value="True"/>
431 </section> 430 </section>
432 <output name="output_html" file="bam-report.html" ftype="html" compare="sim_size" delta="50000"/> 431 <output name="output_html" file="bam-report.html" ftype="html">
432 <assert_contents>
433 <has_text text="html"/>
434 <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
435 </assert_contents>
436 </output>
433 <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/> 437 <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>
434 </test> 438 </test>
435 439 <test><!-- test with multiple input files -->
440 <conditional name="reads">
441 <param name="type" value="fasta"/>
442 <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />
443 </conditional>
444 <output name="output_html" ftype="html">
445 <assert_contents>
446 <has_text text="html"/>
447 <not_has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
448 <has_text text="&lt;td&gt;9.0&lt;/td&gt;"/> <!--check both files used 4+5 reads -->
449 </assert_contents>
450 </output>
451 </test>
436 </tests> 452 </tests>
437 <help> 453 <help>
438 <![CDATA[ 454 <![CDATA[
439
440 **What it does** 455 **What it does**
441 456
442 NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_ 457 NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_
443 458
444 .. _NanoPlot: https://github.com/wdecoster/NanoPlot 459 .. _NanoPlot: https://github.com/wdecoster/NanoPlot