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comparison nanoplot.xml @ 4:edbb6c5028f5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6692949aa694102abb64c67d46196a822fcb61bf"
author iuc
date Sun, 19 Jan 2020 19:03:02 -0500
parents 645159bcee2d
children a3c4fe6f49ab
comparison
equal deleted inserted replaced
3:645159bcee2d 4:edbb6c5028f5
1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1">
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@">1.25.0</token> 4 <token name="@TOOL_VERSION@">1.28.2</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 <version_command>NanoPlot --version</version_command> 9 <version_command>NanoPlot --version</version_command>
61 $filter.drop_outliers 61 $filter.drop_outliers
62 $filter.loglength 62 $filter.loglength
63 $filter.percentqual 63 $filter.percentqual
64 $filter.alength 64 $filter.alength
65 $filter.barcoded 65 $filter.barcoded
66 $customization.noN50
67 $customization.N50 66 $customization.N50
68 -o '.' 67 -o '.'
69 ]]></command> 68 ]]></command>
70 <inputs> 69 <inputs>
71 <conditional name="mode"> 70 <conditional name="mode">
384 <option value="dot">dot</option> 383 <option value="dot">dot</option>
385 <option value="pauvre">pauvre</option> 384 <option value="pauvre">pauvre</option>
386 </param> 385 </param>
387 <param 386 <param
388 type="boolean" 387 type="boolean"
389 name="noN50"
390 truevalue="--no-N50"
391 falsevalue=""
392 label="Hide the N50 mark in the read length histogram."/>
393 <param
394 type="boolean"
395 argument="--N50" 388 argument="--N50"
396 truevalue="--N50" 389 truevalue="--N50"
397 falsevalue="" 390 falsevalue=""
398 label="Show the N50 mark in the read length histogram."/> 391 label="Show the N50 mark in the read length histogram."/>
399 </section> 392 </section>
425 <section name="filter"> 418 <section name="filter">
426 <param name="downsample" value="800"/> 419 <param name="downsample" value="800"/>
427 </section> 420 </section>
428 <section name="customization"> 421 <section name="customization">
429 <param name="plots" value="hex,kde"/> 422 <param name="plots" value="hex,kde"/>
430 <param name="title" value="My Plot"/>
431 </section> 423 </section>
432 <output name="output_html" file="NanoPlot-report.html" ftype="html"/> 424 <output name="output_html" file="NanoPlot-report.html" ftype="html" lines_diff="8" />
433 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/> 425 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>
434 <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/> 426 <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/>
435 </test> 427 </test>
436 <test> 428 <test>
437 <conditional name="mode"> 429 <conditional name="mode">
446 <param name="minlenght" value="1000"/> 438 <param name="minlenght" value="1000"/>
447 </section> 439 </section>
448 <section name="customization"> 440 <section name="customization">
449 <param name="color" value="yellow"/> 441 <param name="color" value="yellow"/>
450 <param name="format" value="svg"/> 442 <param name="format" value="svg"/>
451 <param name="noN50" value="True"/>
452 </section> 443 </section>
453 <output name="output_html" file="bam-report.html" ftype="html"> 444 <output name="output_html" file="bam-report.html" ftype="html" lines_diff="16">
454 <assert_contents> 445 <assert_contents>
455 <has_text text="html"/> 446 <has_text text="html"/>
456 <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific --> 447 <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
457 </assert_contents> 448 </assert_contents>
458 </output> 449 </output>