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comparison dada2_plotQualityProfile.xml @ 2:4095456821e2 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
author matthias
date Tue, 09 Apr 2019 07:03:51 -0400
parents de5c51e1c190
children cf166b8a8e27
comparison
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1:2b8227e68647 2:4095456821e2
1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@"> 1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>plot a visual summary of the quality scores</description> 2 <description>plot a visual summary of the quality scores</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
9 Rscript --slave '$dada2_script' 9 Rscript --slave '$dada2_script'
10 ]]></command> 10 ]]></command>
11 <configfiles> 11 <configfiles>
12 <configfile name="dada2_script"><![CDATA[ 12 <configfile name="dada2_script"><![CDATA[
13 files = c() 13 files = c()
14 #if $mode_cond.mode_select == "TRUE" 14 #if "batch" in $paired_cond.paired_select
15 #for $read in $mode_cond.reads: 15 #if "single" in $paired_cond.paired_select
16 files = c(files, '$read') 16 files = c(files, '$reads')
17 #end for 17 #else
18 files = c(files, '$reads.forward')
19 files = c(files, '$reads.reverse')
20 #end if
18 #else 21 #else
19 files = c(files, '$mode_cond.reads') 22 #for $read in $paired_cond.reads:
23 #if $paired_cond.paired_select == "no"
24 files = c(files, '$read')
25 #else
26 files = c(files, '$read.forward')
27 files = c(files, '$read.reverse')
28 #end if
29 #end for
20 #end if 30 #end if
31
21 32
22 library(ggplot2, quietly=T) 33 library(ggplot2, quietly=T)
23 library(dada2, quietly=T) 34 library(dada2, quietly=T)
24 35
25 qp <- plotQualityProfile(files, 36 qp <- plotQualityProfile(files,
26 #if str($n) != "" 37 #if str($n) != ""
27 n=$n, 38 n=$n,
28 #end if 39 #end if
29 aggregate = $mode_cond.mode_select) 40 aggregate = $mode)
30 41
31 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) 42 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
32 ]]></configfile> 43 ]]></configfile>
33 </configfiles> 44 </configfiles>
34 <inputs> 45 <inputs>
35 <conditional name="mode_cond"> 46 <conditional name="paired_cond">
36 <param name="mode_select" type="select" label="Aggregate data" help="Create a single plot for all data sets (default) or a separate plot for each data set"> 47 <param name="paired_select" type="select" label="Input data organisation and processing mode" help="Select if data is organized in a paired collection or not (note that the pairing of the data sets is not used by the tool); batch will create a separate pdf for each input data set or data set pair; non-batch will create one pdf containing a plot for each data set">
37 <option value="TRUE">yes</option> 48 <option value="paired">paired - non batch</option>
38 <option value="FALSE">no</option> 49 <option value="single">single - non batch</option>
39 </param> 50 <option value="paired_batch">paired - batch</option>
40 <when value="TRUE"> 51 <option value="single_batch">single - batch</option>
41 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> 52 </param>
42 </when> 53 <when value="paired">
43 <when value="FALSE"> 54 <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
44 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> 55 </when>
45 </when> 56 <when value="single">
46 </conditional> 57 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
58 </when>
59 <when value="paired_batch">
60 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
61 </when>
62 <when value="single_batch">
63 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
64 </when>
65 </conditional>
66 <param name="mode" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/>
47 <param name="n" type="integer" optional="true" label="sample number" help="number of records to sample from the fastq file (default 500.000)"/> 67 <param name="n" type="integer" optional="true" label="sample number" help="number of records to sample from the fastq file (default 500.000)"/>
48 </inputs> 68 </inputs>
49 <outputs> 69 <outputs>
50 <data name="output" format="pdf" from_work_dir="output.pdf"/> 70 <data name="output" format="pdf" from_work_dir="output.pdf"/>
51 </outputs> 71 </outputs>
72 <tests>
73 <test>
74 <param name="mode" value="TRUE"/>
75 <conditional name="paired_cond">
76 <param name="paired_select" value="TRUE"/>
77 <param name="reads">
78 <collection type="paired">
79 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
80 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
81 </collection>
82 </param>
83 </conditional>
84 <output name="output" value="qualityProfileMultiple.pdf" ftype="pdf"/>
85 </test>
86 <test>
87 <param name="mode" value="FALSE"/>
88 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
89 <output name="output" value="qualityProfile.pdf" ftype="pdf"/>
90 </test>
91 <test>
92 <param name="mode" value="FALSE"/>
93 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
94 <param name="n" value="10000"/>
95 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
96 </test>
97 </tests>
98 <help><![CDATA[
99 Summary
100 .......
52 101
53 <help><![CDATA[ 102 This function plots a visual summary of the distribution of quality scores as a function of sequence position for the input fastq datasets.
54 TODO: Fill in help. 103
104 Details
105 .......
106
107 The distribution of quality scores at each position is shown as a grey-scale heat map, with dark colors corresponding to higher frequency. The plotted lines show positional summary statistics: green is the mean, orange is the median, and the dashed orange lines are the 25th and 75th quantiles. If the sequences vary in length, a red line will be plotted showing the percentage of reads that extend
108 to at least that position.
109
110 Note this tool ignores the pairing of the reads, but the data is just processed as list.
55 ]]></help> 111 ]]></help>
56 <expand macro="citations"/> 112 <expand macro="citations"/>
57 </tool> 113 </tool>