Mercurial > repos > iuc > vsnp_statistics
comparison vsnp_statistics.xml @ 0:50f539302bf4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
author | iuc |
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date | Fri, 27 Aug 2021 11:46:52 +0000 |
parents | |
children | b960f47c57a1 |
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-1:000000000000 | 0:50f539302bf4 |
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1 <tool id="vsnp_statistics" name="vSNP: statistics" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@"> | |
2 <description></description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="1.79">biopython</requirement> | |
8 <requirement type="package" version="1.21.1">numpy</requirement> | |
9 <requirement type="package" version="3.0.7">openpyxl</requirement> | |
10 <requirement type="package" version="1.3.0">pandas</requirement> | |
11 <requirement type="package" version="2.0.1">xlrd</requirement> | |
12 </requirements> | |
13 <command detect_errors="exit_code"><![CDATA[ | |
14 #import re | |
15 #set input_idxstats_dir = 'input_idxstats' | |
16 #set input_metrics_dir = 'input_metrics' | |
17 #set input_reads_dir = 'input_reads' | |
18 mkdir -p $input_idxstats_dir && | |
19 mkdir -p $input_metrics_dir && | |
20 mkdir -p $input_reads_dir && | |
21 | |
22 #if $input_type_cond.input_type == 'single_files': | |
23 #set read1 = $input_type_cond.read_type_cond.read1 | |
24 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) | |
25 ln -s '${read1}' '${read1_identifier}' && | |
26 #if $input_type_cond.read_type_cond.read_type == 'pair': | |
27 #set read2 = $input_type_cond.read_type_cond.read2 | |
28 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) | |
29 ln -s '${read2}' '${read2_identifier}' && | |
30 #else: | |
31 #set read2 = None | |
32 #end if | |
33 #else: | |
34 #if $input_type_cond.collection_type_cond.collection_type == 'single': | |
35 #for $i in $input_type_cond.collection_type_cond.reads_collection: | |
36 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) | |
37 ln -s '${i.file_name}' '$input_reads_dir/${identifier}' && | |
38 #end for | |
39 #else: | |
40 #set read1 = $input_type_cond.collection_type_cond.reads_collection['forward'] | |
41 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) | |
42 ln -s '${read1}' '$input_reads_dir/${read1_identifier}' && | |
43 #set read2 = $input_type_cond.collection_type_cond.reads_collection['reverse'] | |
44 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name)) | |
45 ln -s '${read2}' '$input_reads_dir/${read2_identifier}' && | |
46 #end if | |
47 #for $i in $input_type_cond.samtools_idxstats: | |
48 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) | |
49 ln -s '${i.file_name}' '$input_idxstats_dir/${identifier}' && | |
50 #end for | |
51 #for $i in $input_type_cond.vsnp_azc: | |
52 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) | |
53 ln -s '${i.file_name}' '$input_metrics_dir/${identifier}' && | |
54 #end for | |
55 #end if | |
56 | |
57 python '$__tool_directory__/vsnp_statistics.py' | |
58 #if $input_type_cond.input_type == 'single_files': | |
59 --dbkey '$input_type_cond.samtools_idxstats.metadata.dbkey' | |
60 #if $input_type_cond.read_type_cond.read1.is_of_type('fastqsanger.gz'): | |
61 --gzipped | |
62 #end if | |
63 --read1 '${read1_identifier}' | |
64 #if $input_type_cond.read_type_cond.read_type == 'pair': | |
65 --read2 '${read2_identifier}' | |
66 #end if | |
67 --samtools_idxstats '$input_type_cond.samtools_idxstats' | |
68 --vsnp_azc '$input_type_cond.vsnp_azc' | |
69 #else: | |
70 --dbkey '$input_type_cond.samtools_idxstats[0].metadata.dbkey' | |
71 #if $input_type_cond.collection_type_cond.reads_collection[0].is_of_type('fastqsanger.gz'): | |
72 --gzipped | |
73 #end if | |
74 #if $input_type_cond.collection_type_cond.collection_type == 'paired': | |
75 --list_paired | |
76 #end if | |
77 --input_idxstats_dir '$input_idxstats_dir' | |
78 --input_metrics_dir '$input_metrics_dir' | |
79 --input_reads_dir '$input_reads_dir' | |
80 #end if | |
81 --output '$output' | |
82 ]]></command> | |
83 <inputs> | |
84 <conditional name="input_type_cond"> | |
85 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> | |
86 <option value="single_files" selected="true">Single files</option> | |
87 <option value="collections">Collections of files</option> | |
88 </param> | |
89 <when value="single_files"> | |
90 <conditional name="read_type_cond"> | |
91 <param name="read_type" type="select" label="Choose the read type"> | |
92 <option value="single" selected="true">Single reads</option> | |
93 <option value="pair">Paired reads</option> | |
94 </param> | |
95 <when value="single"> | |
96 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
97 </when> | |
98 <when value="pair"> | |
99 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
100 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> | |
101 </when> | |
102 </conditional> | |
103 <param name="samtools_idxstats" type="data" format="tabular" label="Samtools idxstats file"/> | |
104 <param name="vsnp_azc" type="data" format="tabular" label="vSNP: add zero coverage metrics file"/> | |
105 </when> | |
106 <when value="collections"> | |
107 <conditional name="collection_type_cond"> | |
108 <param name="collection_type" type="select" label="Collections of single reads or paired reads?"> | |
109 <option value="single" selected="true">Single reads</option> | |
110 <option value="paired">Paired reads in separate datasets</option> | |
111 </param> | |
112 <when value="single"> | |
113 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of fastqsanger files"/> | |
114 </when> | |
115 <when value="paired"> | |
116 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> | |
117 </when> | |
118 </conditional> | |
119 <param name="samtools_idxstats" type="data_collection" format="tabular" collection_type="list" label="Collection of samtools idxstats files"/> | |
120 <param name="vsnp_azc" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP: add zero coverage metrics files"/> | |
121 </when> | |
122 </conditional> | |
123 </inputs> | |
124 <outputs> | |
125 <data name="output" format="tabular"/> | |
126 </outputs> | |
127 <tests> | |
128 <!-- A single fastq file --> | |
129 <test expect_num_outputs="1"> | |
130 <param name="input_type" value="single_files"/> | |
131 <param name="read_type" value="single"/> | |
132 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> | |
133 <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/> | |
134 <param name="vsnp_azc" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/> | |
135 <output name="output" file="vsnp_statistics1.tabular" ftype="tabular"/> | |
136 </test> | |
137 <!-- A set of paired fastq files --> | |
138 <test expect_num_outputs="1"> | |
139 <param name="input_type" value="single_files"/> | |
140 <param name="read_type" value="pair"/> | |
141 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> | |
142 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> | |
143 <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/> | |
144 <param name="vsnp_azc" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/> | |
145 <output name="output" file="vsnp_statistics2.tabular" ftype="tabular"/> | |
146 </test> | |
147 <!-- A collection of SE fastq files --> | |
148 <test expect_num_outputs="1"> | |
149 <param name="input_type" value="collections"/> | |
150 <param name="read_type" value="single"/> | |
151 <param name="reads_collection"> | |
152 <collection type="list"> | |
153 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="Mcap_Deer_DE_SRR650221.fastq.gz" dbkey="89"/> | |
154 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="13-1941-6_S4_L001_R1_600000.fastq.gz" dbkey="89"/> | |
155 </collection> | |
156 </param> | |
157 <param name="samtools_idxstats"> | |
158 <collection type="list"> | |
159 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="samtools_idxstats3.tabular" dbkey="89"/> | |
160 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="samtools_idxstats4.tabular" dbkey="89"/> | |
161 </collection> | |
162 </param> | |
163 <param name="vsnp_azc"> | |
164 <collection type="list"> | |
165 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="add_zc_metrics3.tabular" dbkey="89"/> | |
166 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="add_zc_metrics4.tabular" dbkey="89"/> | |
167 </collection> | |
168 </param> | |
169 <output name="output" file="vsnp_statistics3.tabular" ftype="tabular"/> | |
170 </test> | |
171 <!-- A collection of PE fastq files --> | |
172 <test expect_num_outputs="1"> | |
173 <param name="input_type" value="collections"/> | |
174 <param name="collection_type" value="paired"/> | |
175 <param name="reads_collection"> | |
176 <collection type="paired"> | |
177 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> | |
178 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/> | |
179 </collection> | |
180 </param> | |
181 <param name="samtools_idxstats"> | |
182 <collection type="list"> | |
183 <element name="13-1941-6_S4_L001_R1_600000.fastq" value="samtools_idxstats5.tabular" dbkey="89"/> | |
184 </collection> | |
185 </param> | |
186 <param name="vsnp_azc"> | |
187 <collection type="list"> | |
188 <element name="13-1941-6_S4_L001_R1_600000.fastq" value="add_zc_metrics5.tabular" dbkey="89"/> | |
189 </collection> | |
190 </param> | |
191 <output name="output" file="vsnp_statistics4.tabular" ftype="tabular"/> | |
192 </test> | |
193 </tests> | |
194 <help> | |
195 **What it does** | |
196 | |
197 Accepts associated fastq files, SAMtools idxstats files and **vSNP: add zero coverage** metrics files and extracts information from them | |
198 to produce an Excel spreadsheet containing statistics for each sample. The samples can be single or paired reads, and all associated inputs | |
199 can be either single files or collections of files. The output statistics include reference, file size, mean read length, mean read quality, | |
200 reads passing Q30, total reads, all mapped reads, unmapped reads, unmapped reads percentage of total, reference with coverage, average depth | |
201 of coverage and good SNP count. | |
202 </help> | |
203 <expand macro="citations"/> | |
204 </tool> | |
205 |