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comparison vsnp_statistics.xml @ 1:14e29f7d59ca draft

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author greg
date Wed, 29 Apr 2020 16:56:10 -0400
parents c21d338dbdc4
children 7fe0cbb8c894
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0:c21d338dbdc4 1:14e29f7d59ca
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.1">humanize</requirement> 4 <requirement type="package" version="0.5.1">humanize</requirement>
5 <requirement type="package" version="1.16.5">numpy</requirement> 5 <requirement type="package" version="1.16.5">numpy</requirement>
6 <requirement type="package" version="0.25.3">pandas</requirement> 6 <requirement type="package" version="0.25.3">pandas</requirement>
7 <requirement type="package" version="1.2.0">xlrd</requirement>
8 <requirement type="package" version="1.2.8">xlsxwriter</requirement>
7 </requirements> 9 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
9 #import os 11 #import os
10 #import re 12 #import re
11 #set gzipped = 'false' 13 #set gzipped = 'false'
12 #set input_type = $input_type_cond.input_type 14 #set input_type = $input_type_cond.input_type
13 #set input_idxstats_dir = 'input_idxstats' 15 #set input_idxstats_dir = 'input_idxstats'
14 #set input_metrics_dir = 'input_metrics' 16 #set input_metrics_dir = 'input_metrics'
15 #set input_reads_dir = 'input_reads' 17 #set input_reads_dir = 'input_reads'
16 #set output_dir = 'output'
17 mkdir -p $input_idxstats_dir && 18 mkdir -p $input_idxstats_dir &&
18 mkdir -p $input_metrics_dir && 19 mkdir -p $input_metrics_dir &&
19 mkdir -p $input_reads_dir && 20 mkdir -p $input_reads_dir &&
20 mkdir -p $output_dir &&
21 #if str($input_type) == "single": 21 #if str($input_type) == "single":
22 #set read_type_cond = $input_type_cond.read_type_cond 22 #set read_type_cond = $input_type_cond.read_type_cond
23 #set read1 = $read_type_cond.read1 23 #set read1 = $read_type_cond.read1
24 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) 24 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
25 #if str($read_type_cond.read_type) == "single": 25 #if str($read_type_cond.read_type) == "single":
42 #if $i.is_of_type('fastqsanger.gz'): 42 #if $i.is_of_type('fastqsanger.gz'):
43 #set gzipped = 'true' 43 #set gzipped = 'true'
44 #end if 44 #end if
45 #set filename = $i.file_name 45 #set filename = $i.file_name
46 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) 46 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
47 ln -s $filename $input_reads_dir/$identifier && 47 ln -s '$filename' '$input_reads_dir/$identifier' &&
48 #end for 48 #end for
49 #for $i in $input_type_cond.samtools_idxstats_collection: 49 #for $i in $input_type_cond.samtools_idxstats_collection:
50 #set filename = $i.file_name 50 #set filename = $i.file_name
51 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) 51 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
52 ln -s $filename $input_idxstats_dir/$identifier && 52 ln -s '$filename' '$input_idxstats_dir/$identifier' &&
53 #end for 53 #end for
54 #for $i in $input_type_cond.azc_metrics_collection: 54 #for $i in $input_type_cond.azc_metrics_collection:
55 #set dbkey = $i.metadata.dbkey 55 #set dbkey = $i.metadata.dbkey
56 #set filename = $i.file_name 56 #set filename = $i.file_name
57 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) 57 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
58 ln -s $filename $input_metrics_dir/$identifier && 58 ln -s '$filename' '$input_metrics_dir/$identifier' &&
59 #end for 59 #end for
60 #end if 60 #end if
61 python '$__tool_directory__/vsnp_statistics.py' 61 python '$__tool_directory__/vsnp_statistics.py'
62 --processes $processes
63 --dbkey '$dbkey' 62 --dbkey '$dbkey'
64 --gzipped '$gzipped' 63 --gzipped '$gzipped'
65 #if str($input_type) == "single": 64 #if str($input_type) == "single":
66 #if str($read_type_cond.read_type) == "single": 65 #if str($read_type_cond.read_type) == "single":
67 --read1 '${read1_identifier}' 66 --read1 '${read1_identifier}'
69 --read1 '${read1_identifier}' 68 --read1 '${read1_identifier}'
70 --read2 '${read2_identifier}' 69 --read2 '${read2_identifier}'
71 #end if 70 #end if
72 --samtools_idxstats '$samtools_idxstats' 71 --samtools_idxstats '$samtools_idxstats'
73 --vsnp_azc '$vsnp_azc' 72 --vsnp_azc '$vsnp_azc'
74 --output '$output'
75 #end if 73 #end if
74 --output '$output'
76 ]]></command> 75 ]]></command>
77 <inputs> 76 <inputs>
78 <conditional name="input_type_cond"> 77 <conditional name="input_type_cond">
79 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> 78 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
80 <option value="single" selected="true">Single files</option> 79 <option value="single" selected="true">Single files</option>
105 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of fastqsanger files"/> 104 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of fastqsanger files"/>
106 <param name="samtools_idxstats_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of samtools idxstats files"/> 105 <param name="samtools_idxstats_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of samtools idxstats files"/>
107 <param name="azc_metrics_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP zero-coverage metrics files"/> 106 <param name="azc_metrics_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP zero-coverage metrics files"/>
108 </when> 107 </when>
109 </conditional> 108 </conditional>
110 <param name="processes" type="integer" min="1" max="20" value="8" label="Number of processes for job splitting"/>
111 </inputs> 109 </inputs>
112 <outputs> 110 <outputs>
113 <data name="output" format="tabular"> 111 <data name="output" format="xlsx"/>
114 <filter>input_type_cond['input_type'] == 'single'</filter>
115 </data>
116 <collection name="output_collection" type="list">
117 <discover_datasets pattern="__name__" directory="output" format="tabular" />
118 <filter>input_type_cond['input_type'] == 'collection'</filter>
119 </collection>
120 </outputs> 112 </outputs>
121 <tests> 113 <tests>
122 <test> 114 <test>
123 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> 115 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
124 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> 116 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
125 <param name="samtools_idxstats" value="samtools_idxstats.tabular" ftype="tabular" dbkey="89"/> 117 <param name="samtools_idxstats" value="samtools_idxstats.tabular" ftype="tabular" dbkey="89"/>
126 <param name="vsnp_azc" value="add_zc_metrics.tabular" ftype="tabular" dbkey="89"/> 118 <param name="vsnp_azc" value="add_zc_metrics.tabular" ftype="tabular" dbkey="89"/>
127 <output name="output" file="vsnp_statistics.tabular" ftype="tabular" compare="contains"/> 119 <output name="output" file="vsnp_statistics.xlsx" ftype="xlsx" compare="sim_size"/>
128 </test> 120 </test>
129 </tests> 121 </tests>
130 <help> 122 <help>
131 **What it does** 123 **What it does**
132 124
136 of coverage, good SNP count and more. 128 of coverage, good SNP count and more.
137 129
138 **Required options** 130 **Required options**
139 131
140 * **Choose the type for files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single or paired fastqsanger reads or collections of fastqsanger reads and associated idxstats and vSNP zero coverage metrics files) based on the selected option.. 132 * **Choose the type for files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single or paired fastqsanger reads or collections of fastqsanger reads and associated idxstats and vSNP zero coverage metrics files) based on the selected option..
141 * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time.
142 </help> 133 </help>
143 <citations> 134 <citations>
144 <citation type="bibtex"> 135 <citation type="bibtex">
145 @misc{None, 136 @misc{None,
146 journal = {None}, 137 journal = {None},