Mercurial > repos > matthias > dada2_plotqualityprofile
comparison dada2_plotQualityProfile.xml @ 5:863ebf0d28d5 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
author | matthias |
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date | Sun, 05 May 2019 12:26:15 -0400 |
parents | cf166b8a8e27 |
children | ec0479593908 |
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4:4be2c17fd0b2 | 5:863ebf0d28d5 |
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4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="version_command"/> | 7 <expand macro="version_command"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 Rscript --slave '$dada2_script' | 9 ##name files by linking |
10 #import re | |
11 #if "batch" in str($paired_cond.paired_select) | |
12 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier)) | |
13 #if "single" in str($paired_cond.paired_select) | |
14 ln -s '$paired_cond.fl' '$elid' && | |
15 #else | |
16 ln -s '$paired_cond.fl.forward' '$elid'_forward && | |
17 ln -s '$paired_cond.fl.reverse' '$elid'_reverse && | |
18 #end if | |
19 #else | |
20 #for $read in $paired_cond.fl: | |
21 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) | |
22 #if "single" in str($paired_cond.paired_select) | |
23 ln -s '$read' '$elid' && | |
24 #else | |
25 ln -s '$read.forward' '$elid'_forward && | |
26 ln -s '$read.reverse' '$elid'_reverse && | |
27 #end if | |
28 #end for | |
29 #end if | |
30 | |
31 Rscript --slave '$dada2_script' | |
10 ]]></command> | 32 ]]></command> |
11 <configfiles> | 33 <configfiles> |
12 <configfile name="dada2_script"><![CDATA[ | 34 <configfile name="dada2_script"><![CDATA[ |
35 #import re | |
13 files = c() | 36 files = c() |
14 #if "batch" in str($paired_cond.paired_select) | 37 #if "batch" in str($paired_cond.paired_select) |
38 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier)) | |
15 #if "single" in str($paired_cond.paired_select) | 39 #if "single" in str($paired_cond.paired_select) |
16 files = c(files, '$paired_cond.reads') | 40 files = c(files, '$elid') |
17 #else | 41 #else |
18 files = c(files, '$paired_cond.reads.forward') | 42 files = c(files, paste('$elid', 'forward', sep = "_")) |
19 files = c(files, '$paired_cond.reads.reverse') | 43 files = c(files, paste('$elid', 'reverse', sep = "_")) |
20 #end if | 44 #end if |
21 #else | 45 #else |
22 #for $read in $paired_cond.reads: | 46 #for $read in $paired_cond.fl: |
47 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) | |
23 #if "single" in str($paired_cond.paired_select) | 48 #if "single" in str($paired_cond.paired_select) |
24 files = c(files, '$read') | 49 files = c(files, '$elid') |
25 #else | 50 #else |
26 files = c(files, '$read.forward') | 51 files = c(files, paste('$elid', 'forward', sep = "_")) |
27 files = c(files, '$read.reverse') | 52 files = c(files, paste('$elid', 'reverse', sep = "_")) |
28 #end if | 53 #end if |
29 #end for | 54 #end for |
30 #end if | 55 #end if |
31 | 56 |
32 library(ggplot2, quietly=T) | 57 library(ggplot2, quietly=T) |
48 <option value="single">single - non batch</option> | 73 <option value="single">single - non batch</option> |
49 <option value="paired_batch">paired - batch</option> | 74 <option value="paired_batch">paired - batch</option> |
50 <option value="single_batch">single - batch</option> | 75 <option value="single_batch">single - batch</option> |
51 </param> | 76 </param> |
52 <when value="paired"> | 77 <when value="paired"> |
53 <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> | 78 <param argument="fl" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
54 </when> | 79 </when> |
55 <when value="single"> | 80 <when value="single"> |
56 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> | 81 <param argument="fl" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
57 </when> | 82 </when> |
58 <when value="paired_batch"> | 83 <when value="paired_batch"> |
59 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> | 84 <param argument="fl" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
60 </when> | 85 </when> |
61 <when value="single_batch"> | 86 <when value="single_batch"> |
62 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> | 87 <param argument="fl" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
63 </when> | 88 </when> |
64 </conditional> | 89 </conditional> |
65 <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"/> | 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"/> |
66 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/> | 91 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/> |
67 </inputs> | 92 </inputs> |
71 <tests> | 96 <tests> |
72 <!-- paired non-batch, aggregate --> | 97 <!-- paired non-batch, aggregate --> |
73 <test> | 98 <test> |
74 <param name="aggregate" value="TRUE"/> | 99 <param name="aggregate" value="TRUE"/> |
75 <param name="paired_cond|paired_select" value="paired"/> | 100 <param name="paired_cond|paired_select" value="paired"/> |
76 <param name="paired_cond|reads"> | 101 <param name="paired_cond|fl"> |
77 <collection type="list:paired"> | 102 <collection type="list:paired"> |
78 <element name="F3D0_S188_L001"> | 103 <element name="F3D0_S188_L001"> |
79 <collection type="paired"> | 104 <collection type="paired"> |
80 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> | 105 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
81 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> | 106 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
87 </test> | 112 </test> |
88 <!-- paired, batch, no aggregate--> | 113 <!-- paired, batch, no aggregate--> |
89 <test> | 114 <test> |
90 <param name="aggregate" value="FALSE"/> | 115 <param name="aggregate" value="FALSE"/> |
91 <param name="paired_cond|paired_select" value="paired_batch"/> | 116 <param name="paired_cond|paired_select" value="paired_batch"/> |
92 <param name="paired_cond|reads"> | 117 <param name="paired_cond|fl"> |
93 <collection type="paired"> | 118 <collection type="paired"> |
94 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> | 119 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
95 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> | 120 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
96 </collection> | 121 </collection> |
97 </param> | 122 </param> |
99 </test> | 124 </test> |
100 <!-- single, non-batch, aggregate --> | 125 <!-- single, non-batch, aggregate --> |
101 <test> | 126 <test> |
102 <param name="aggregate" value="TRUE"/> | 127 <param name="aggregate" value="TRUE"/> |
103 <param name="paired_cond|paired_select" value="single"/> | 128 <param name="paired_cond|paired_select" value="single"/> |
104 <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> | 129 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
105 <param name="n" value="10000"/> | 130 <param name="n" value="10000"/> |
106 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/> | 131 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/> |
107 </test> | 132 </test> |
108 <!-- single, batch, no aggregate --> | 133 <!-- single, batch, no aggregate --> |
109 <test> | 134 <test> |
110 <param name="aggregate" value="FALSE"/> | 135 <param name="aggregate" value="FALSE"/> |
111 <param name="paired_cond|paired_select" value="single_batch"/> | 136 <param name="paired_cond|paired_select" value="single_batch"/> |
112 <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> | 137 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
113 <param name="n" value="10000"/> | 138 <param name="n" value="10000"/> |
114 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/> | 139 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/> |
115 </test> </tests> | 140 </test> </tests> |
116 <help><![CDATA[ | 141 <help><![CDATA[ |
117 Summary | 142 Summary |