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comparison nanoplot.xml @ 3:645159bcee2d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
author iuc
date Fri, 21 Jun 2019 19:13:55 -0400
parents acd337269171
children edbb6c5028f5
comparison
equal deleted inserted replaced
2:acd337269171 3:645159bcee2d
1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0"> 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@">1.25.0</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>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code"><![CDATA[
11 <![CDATA[ 11 #set $myfiles = $mode.reads.files
12 12
13 #set reads_temp = [] 13 #set reads_temp = []
14 #for $i, $f in enumerate($reads.files) 14 #if $mode.choice == 'combined':
15 #for $i, $f in enumerate($myfiles)
16 #if $f.ext == "fastqsanger":
17 #set $extension = 'fastq'
18 #else
15 #set $extension = $f.ext 19 #set $extension = $f.ext
16 #if $extension == 'fastqsanger' 20 #end if
17 #set $extension = 'fastq' 21 ln -s '$f' './read_${i}.$extension' &&
18 #end if 22 $reads_temp.append("read_" + str($i) + "." + str($extension))
19 ln -s '$f' './read_${i}.$extension' && 23 #end for
20 $reads_temp.append("read_" + str($i) + "." + str($extension)) 24 #else
21 #end for 25 #if $myfiles.ext == "fastqsanger":
22 26 #set $extension = 'fastq'
23 NanoPlot 27 #else
24 --threads \${GALAXY_SLOTS:-4} 28 #set $extension = $myfiles.ext
25 --$reads.type ${' '.join($reads_temp)} 29 #end if
26 30 ln -s '$mode.reads.files' './read.$extension' &&
27 #if $filter.maxlength 31 $reads_temp.append("read." + str($extension))
28 --maxlength $filter.maxlength 32 #end if
29 #end if 33
30 #if $filter.minlength 34 NanoPlot
31 --minlength $filter.minlength 35 --threads \${GALAXY_SLOTS:-4}
32 #end if 36 --$mode.reads.type ${' '.join($reads_temp)}
33 #if $filter.downsample 37 #if $filter.maxlength
34 --downsample $filter.downsample 38 --maxlength $filter.maxlength
35 #end if 39 #end if
36 #if $filter.minqual 40 #if $filter.minlength
37 --minqual $filter.minqual 41 --minlength $filter.minlength
38 #end if 42 #end if
39 #if $filter.readtype 43 #if $filter.downsample
40 --readtype $filter.readtype 44 --downsample $filter.downsample
41 #end if 45 #end if
42 #if $customization.color 46 #if $filter.minqual
43 --color $customization.color 47 --minqual $filter.minqual
44 #end if 48 #end if
45 #if $customization.format 49 #if $filter.readtype
46 --format $customization.format 50 --readtype $filter.readtype
47 #end if 51 #end if
48 #if $customization.plots 52 #if $customization.color
49 --plots ${str($customization.plots).replace(',', ' ')} 53 --color $customization.color
50 #end if 54 #end if
51 $filter.drop_outliers 55 #if $customization.format
52 $filter.loglength 56 --format $customization.format
53 $filter.percentqual 57 #end if
54 $filter.alength 58 #if $customization.plots
55 $filter.barcoded 59 --plots ${str($customization.plots).replace(',', ' ')}
56 $customization.noN50 60 #end if
57 $customization.N50 61 $filter.drop_outliers
58 -o '.' 62 $filter.loglength
59 ]]> 63 $filter.percentqual
60 </command> 64 $filter.alength
65 $filter.barcoded
66 $customization.noN50
67 $customization.N50
68 -o '.'
69 ]]></command>
61 <inputs> 70 <inputs>
62 <conditional name="reads"> 71 <conditional name="mode">
63 <param name="type" type="select" label="Type of the file(s) to work on"> 72 <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.">
64 <option value="fastq" selected="true">fastq</option> 73 <option value="batch" selected="true">batch</option>
65 <option value="fasta">fasta</option> 74 <option value="combined">combined</option>
66 <option value="fastq_rich">fastq_rich</option>
67 <option value="fastq_minimal">fastq_minimal</option>
68 <option value="summary">summary</option>
69 <option value="bam">bam</option>
70 <option value="cram">cram</option>
71 </param> 75 </param>
72 <when value="fastq"> 76 <when value="batch">
73 <param 77 <conditional name="reads">
74 type="data" 78 <param name="type" type="select" label="Type of the file(s) to work on">
75 argument="--fastq" 79 <option value="fastq" selected="true">fastq</option>
76 name="files" 80 <option value="fasta">fasta</option>
77 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" 81 <option value="fastq_rich">fastq_rich</option>
78 multiple="true"/> 82 <option value="fastq_minimal">fastq_minimal</option>
83 <option value="summary">summary</option>
84 <option value="bam">bam</option>
85 <option value="cram">cram</option>
86 </param>
87 <when value="fastq">
88 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
89 </when>
90 <when value="fasta">
91 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip"/>
92 </when>
93 <when value="fastq_rich">
94 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
95 </when>
96 <when value="fastq_minimal">
97 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
98 </when>
99 <when value="summary">
100 <param type="data" argument="--summary" name="files" format="txt,zip"/>
101 </when>
102 <when value="bam">
103 <param type="data" argument="--bam" name="files" format="bam"/>
104 </when>
105 <when value="cram">
106 <param type="data" argument="--cram" name="files" format="cram"/>
107 </when>
108 </conditional>
79 </when> 109 </when>
80 <when value="fasta"> 110 <when value="combined">
81 <param 111 <conditional name="reads">
82 type="data" 112 <param name="type" type="select" label="Type of the file(s) to work on">
83 argument="--fasta" 113 <option value="fastq" selected="true">fastq</option>
84 name="files" 114 <option value="fasta">fasta</option>
85 format="fasta,fasta.gz,vcf_bgzip" 115 <option value="fastq_rich">fastq_rich</option>
86 multiple="true"/> 116 <option value="fastq_minimal">fastq_minimal</option>
87 </when> 117 <option value="summary">summary</option>
88 <when value="fastq_rich"> 118 <option value="bam">bam</option>
89 <param 119 <option value="cram">cram</option>
90 type="data" 120 </param>
91 argument="--fastq_rich" 121 <when value="fastq">
92 name="files" 122 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
93 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" 123 </when>
94 multiple="true"/> 124 <when value="fasta">
95 </when> 125 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip" multiple="true"/>
96 <when value="fastq_minimal"> 126 </when>
97 <param 127 <when value="fastq_rich">
98 type="data" 128 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
99 argument="--fastq_minimal" 129 </when>
100 name="files" 130 <when value="fastq_minimal">
101 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" 131 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
102 multiple="true"/> 132 </when>
103 </when> 133 <when value="summary">
104 <when value="summary"> 134 <param type="data" argument="--summary" name="files" format="txt,zip" multiple="true"/>
105 <param 135 </when>
106 type="data" 136 <when value="bam">
107 argument="--summary" 137 <param type="data" argument="--bam" name="files" format="bam" multiple="true"/>
108 name="files" 138 </when>
109 format="txt,zip" 139 <when value="cram">
110 multiple="true"/> 140 <param type="data" argument="--cram" name="files" format="cram" multiple="true"/>
111 </when> 141 </when>
112 <when value="bam"> 142 </conditional>
113 <param
114 type="data"
115 argument="--bam"
116 name="files"
117 format="bam"
118 multiple="true"/>
119 </when>
120 <when value="cram">
121 <param
122 type="data"
123 argument="--cram"
124 name="files"
125 format="cram"
126 multiple="true"/>
127 </when> 143 </when>
128 </conditional> 144 </conditional>
129 <section 145 <section
130 name="filter" 146 name="filter"
131 title="Options for filtering or transforming input prior to plotting" 147 title="Options for filtering or transforming input prior to plotting"
397 </change_format> 413 </change_format>
398 </data> 414 </data>
399 </outputs> 415 </outputs>
400 <tests> 416 <tests>
401 <test> 417 <test>
402 <conditional name="reads"> 418 <conditional name="mode">
403 <param name="type" value="fastq_rich"/> 419 <param name="choice" value="batch"/>
404 <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/> 420 <conditional name="reads">
421 <param name="type" value="fastq_rich"/>
422 <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/>
423 </conditional>
405 </conditional> 424 </conditional>
406 <section name="filter"> 425 <section name="filter">
407 <param name="downsample" value="800"/> 426 <param name="downsample" value="800"/>
408 </section> 427 </section>
409 <section name="customization"> 428 <section name="customization">
413 <output name="output_html" file="NanoPlot-report.html" ftype="html"/> 432 <output name="output_html" file="NanoPlot-report.html" ftype="html"/>
414 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/> 433 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>
415 <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/> 434 <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/>
416 </test> 435 </test>
417 <test> 436 <test>
418 <conditional name="reads"> 437 <conditional name="mode">
419 <param name="type" value="bam"/> 438 <param name="choice" value="combined"/>
420 <param name="files" value="alignment.bam" ftype="bam"/> 439 <conditional name="reads">
440 <param name="type" value="bam"/>
441 <param name="files" value="alignment.bam" ftype="bam"/>
442 </conditional>
421 </conditional> 443 </conditional>
422 <section name="filter"> 444 <section name="filter">
423 <param name="maxlength" value="2000"/> 445 <param name="maxlength" value="2000"/>
424 <param name="minlenght" value="1000"/> 446 <param name="minlenght" value="1000"/>
425 </section> 447 </section>
435 </assert_contents> 457 </assert_contents>
436 </output> 458 </output>
437 <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/> 459 <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>
438 </test> 460 </test>
439 <test><!-- test with multiple input files --> 461 <test><!-- test with multiple input files -->
440 <conditional name="reads"> 462 <conditional name="mode">
441 <param name="type" value="fasta"/> 463 <param name="choice" value="combined"/>
442 <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" /> 464 <conditional name="reads">
465 <param name="type" value="fasta"/>
466 <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />
467 </conditional>
443 </conditional> 468 </conditional>
444 <output name="output_html" ftype="html"> 469 <output name="output_html" ftype="html">
445 <assert_contents> 470 <assert_contents>
446 <has_text text="html"/> 471 <has_text text="html"/>
447 <not_has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific --> 472 <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 --> 473 <has_text text="&lt;td&gt;9.0&lt;/td&gt;"/> <!--check both files were used 4+5 reads -->
449 </assert_contents> 474 </assert_contents>
450 </output> 475 </output>
451 </test> 476 </test>
452 </tests> 477 </tests>
453 <help> 478 <help>