Mercurial > repos > matthias > dada2_plotqualityprofile

comparison dada2_plotQualityProfile.xml @ 8:7970dfbedde3 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 977f22125c9ad5c3c5560de8946017305c5633c1
author matthias
date Mon, 27 May 2019 13:23:01 -0400
parents ec0479593908
children d908015e5889
comparison
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7:ec0479593908 8:7970dfbedde3
31 Rscript --slave '$dada2_script' 31 Rscript --slave '$dada2_script'
32 ]]></command> 32 ]]></command>
33 <configfiles> 33 <configfiles>
34 <configfile name="dada2_script"><![CDATA[ 34 <configfile name="dada2_script"><![CDATA[
35 #import re 35 #import re
36 files = c() 36 fwd_files = c()
37 rev_files = c()
37 #if "batch" in str($paired_cond.paired_select) 38 #if "batch" in str($paired_cond.paired_select)
38 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier)) 39 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier))
39 #if "single" in str($paired_cond.paired_select) 40 #if "single" in str($paired_cond.paired_select)
40 files = c(files, '$elid') 41 fwd_files = c(fwd_files, '$elid')
41 #else 42 #else
42 files = c(files, paste('$elid', 'forward', sep = "_")) 43 fwd_files = c(fwd_files, paste('$elid', 'forward', sep = "_"))
43 files = c(files, paste('$elid', 'reverse', sep = "_")) 44 rev_files = c(rev_files, paste('$elid', 'reverse', sep = "_"))
44 #end if 45 #end if
45 #else 46 #else
46 #for $read in $paired_cond.fl: 47 #for $read in $paired_cond.fl:
47 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) 48 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
48 #if "single" in str($paired_cond.paired_select) 49 #if "single" in str($paired_cond.paired_select)
49 files = c(files, '$elid') 50 fwd_files = c(fwd_files, '$elid')
50 #else 51 #else
51 files = c(files, paste('$elid', 'forward', sep = "_")) 52 fwd_files = c(fwd_files, paste('$elid', 'forward', sep = "_"))
52 files = c(files, paste('$elid', 'reverse', sep = "_")) 53 rev_files = c(rev_files, paste('$elid', 'reverse', sep = "_"))
53 #end if 54 #end if
54 #end for 55 #end for
56 #end if
57
58 #if not "batch" in str($paired_cond.paired_select)
59 agg = $paired_cond.aggregate
60 #else
61 agg = FALSE
55 #end if 62 #end if
56 63
57 library(ggplot2, quietly=T) 64 library(ggplot2, quietly=T)
58 library(dada2, quietly=T) 65 library(dada2, quietly=T)
59 66
60 qp <- plotQualityProfile(files, 67 qp <- plotQualityProfile(fwd_files,
61 #if str($n) != "" 68 #if str($n) != ""
62 n=$n, 69 n=$n,
63 #end if 70 #end if
64 aggregate = $aggregate) 71 aggregate = agg)
72 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
65 73
66 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) 74 #if "paired" in str($paired_cond.paired_select)
75 qp <- plotQualityProfile(rev_files,
76 #if str($n) != ""
77 n=$n,
78 #end if
79 aggregate = agg)
80 ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
81 #end if
67 ]]></configfile> 82 ]]></configfile>
68 </configfiles> 83 </configfiles>
69 <inputs> 84 <inputs>
70 <conditional name="paired_cond"> 85 <conditional name="paired_cond">
71 <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"> 86 <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">
74 <option value="paired_batch">paired - batch</option> 89 <option value="paired_batch">paired - batch</option>
75 <option value="single_batch">single - batch</option> 90 <option value="single_batch">single - batch</option>
76 </param> 91 </param>
77 <when value="paired"> 92 <when value="paired">
78 <param argument="fl" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="Short read data"/> 93 <param argument="fl" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="Short read data"/>
94 <param argument="aggregate" 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"/>
79 </when> 95 </when>
80 <when value="single"> 96 <when value="single">
81 <param argument="fl" type="data" multiple="true" format="fastq,fastq.gz" label="Short read data"/> 97 <param argument="fl" type="data" multiple="true" format="fastq,fastq.gz" label="Short read data"/>
98 <param argument="aggregate" 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"/>
82 </when> 99 </when>
83 <when value="paired_batch"> 100 <when value="paired_batch">
84 <param argument="fl" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Short read data"/> 101 <param argument="fl" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Short read data"/>
85 </when> 102 </when>
86 <when value="single_batch"> 103 <when value="single_batch">
87 <param argument="fl" type="data" format="fastq,fastq.gz" label="Short read data"/> 104 <param argument="fl" type="data" format="fastq,fastq.gz" label="Short read data"/>
88 </when> 105 </when>
89 </conditional> 106 </conditional>
90 <param argument="aggregate" 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"/>
91 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/> 107 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/>
92 </inputs> 108 </inputs>
93 <outputs> 109 <outputs>
94 <data name="output" format="pdf" from_work_dir="output.pdf"/> 110 <data name="output" format="pdf" from_work_dir="output.pdf">
111 <filter>"single" in paired_cond['paired_select']</filter>
112 </data>
113 <data name="output_fwd" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
114 <filter>"paired" in paired_cond['paired_select']</filter>
115 </data>
116 <data name="output_rev" format="pdf" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
117 <filter>"paired" in paired_cond['paired_select']</filter>
118 </data>
95 </outputs> 119 </outputs>
96 <tests> 120 <tests>
97 <!-- paired non-batch, aggregate --> 121 <!-- paired non-batch, aggregate -->
98 <test> 122 <test>
99 <param name="aggregate" value="TRUE"/>
100 <param name="paired_cond|paired_select" value="paired"/> 123 <param name="paired_cond|paired_select" value="paired"/>
124 <param name="paired_cond|aggregate" value="TRUE"/>
101 <param name="paired_cond|fl"> 125 <param name="paired_cond|fl">
102 <collection type="list:paired"> 126 <collection type="list:paired">
103 <element name="F3D0_S188_L001"> 127 <element name="F3D0_S188_L001">
104 <collection type="paired"> 128 <collection type="paired">
105 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 129 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
106 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 130 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
107 </collection> 131 </collection>
108 </element> 132 </element>
109 </collection> 133 </collection>
110 </param> 134 </param>
111 <output name="output" value="qualityProfileMultiple.pdf" ftype="pdf"/> 135 <output name="output_fwd" value="qualityProfileMultiple.pdf" ftype="pdf"/>
136 <output name="output_rev" value="qualityProfileMultiple_rev.pdf" ftype="pdf"/>
112 </test> 137 </test>
113 <!-- paired, batch, no aggregate--> 138 <!-- paired, batch, no aggregate-->
114 <test> 139 <test>
115 <param name="aggregate" value="FALSE"/>
116 <param name="paired_cond|paired_select" value="paired_batch"/> 140 <param name="paired_cond|paired_select" value="paired_batch"/>
117 <param name="paired_cond|fl"> 141 <param name="paired_cond|fl">
118 <collection type="paired"> 142 <collection type="paired">
119 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 143 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
120 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 144 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
121 </collection> 145 </collection>
122 </param> 146 </param>
123 <output name="output" value="qualityProfile.pdf" ftype="pdf"/> 147 <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf"/>
148 <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf"/>
124 </test> 149 </test>
125 <!-- single, non-batch, aggregate --> 150 <!-- single, non-batch, aggregate -->
126 <test> 151 <test>
127 <param name="aggregate" value="TRUE"/>
128 <param name="paired_cond|paired_select" value="single"/> 152 <param name="paired_cond|paired_select" value="single"/>
153 <param name="paired_cond|aggregate" value="TRUE"/>
129 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 154 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
130 <param name="n" value="10000"/> 155 <param name="n" value="10000"/>
131 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/> 156 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
132 </test> 157 </test>
133 <!-- single, batch, no aggregate --> 158 <!-- single, batch, no aggregate -->