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comparison stacks_ustacks.xml @ 6:35a41f8e1c41 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:14:18 -0400
parents 74a205bb4d66
children e10c08abf18f
comparison
equal deleted inserted replaced
5:901728c2661d 6:35a41f8e1c41
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="stdio"/> 7 <expand macro="stdio"/>
8 <command><![CDATA[ 8 <command><![CDATA[
9 #from os.path import splitext 9
10 #import re 10 @CLEAN_EXT@
11 11
12 mkdir stacks_inputs stacks_outputs 12 mkdir stacks_inputs stacks_outputs
13 13
14 && 14 &&
15 15
16 #if $sample.is_of_type('fastqsanger'): 16 #if $sample.is_of_type('fastqsanger')
17 #set $data_path = splitext($sample.element_identifier)[0] 17 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fq"
18 #set $data_path = re.sub(r'\.1$', '', $data_path)
19 #set $data_path = "stacks_inputs/" + $data_path + ".fq"
20 #set inputype = "fastq" 18 #set inputype = "fastq"
21 #else: 19 #else if $sample.is_of_type('fastqsanger.gz')
22 #set $data_path = splitext($sample.element_identifier)[0] 20 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fq.gz"
23 #set $data_path = re.sub(r'\.1$', '', $data_path) 21 #set inputype = "gzfastq"
24 #set $data_path = "stacks_inputs/" + $data_path + ".fa" 22 #else
23 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fa"
25 #set inputype = "fasta" 24 #set inputype = "fasta"
26 #end if 25 #end if
27 26
28 ln -s "${sample}" "${data_path}" 27 ln -s '${sample}' '${data_path}'
29 28
30 && 29 &&
31 30
32 ustacks 31 ustacks
33 32
44 -M $M 43 -M $M
45 $R 44 $R
46 $H 45 $H
47 46
48 ## Assembly 47 ## Assembly
49 $assembly_options.r 48 $assembly_options.keep_high_cov
50 $assembly_options.d 49 $assembly_options.d
51 --max_locus_stacks $assembly_options.max_locus_stacks 50 --max_locus_stacks $assembly_options.max_locus_stacks
52 #if str($assembly_options.k_len): 51 #if str($assembly_options.k_len)
53 --k_len $assembly_options.k_len 52 --k_len $assembly_options.k_len
54 #end if 53 #end if
55 54
56 #if $gapped.use_gapped: 55 #if $gapped.use_gapped == "yes"
57 --gapped 56 --gapped
58 --max_gaps $gapped.max_gaps 57 --max_gaps $gapped.max_gaps
59 --min_aln_len $gapped.min_aln_len 58 --min_aln_len $gapped.min_aln_len
60 #end if 59 #end if
61 60
62 ## snp_model 61 ## snp_model
63 #if str( $snp_options.select_model.model_type) == "bounded": 62 #if str( $snp_options.select_model.model_type) == "bounded"
64 --model_type bounded 63 --model_type bounded
65 --bound_low $snp_options.select_model.bound_low 64 --bound_low $snp_options.select_model.bound_low
66 --bound_high $snp_options.select_model.bound_high 65 --bound_high $snp_options.select_model.bound_high
67 --alpha $snp_options.select_model.alpha 66 --alpha $snp_options.select_model.alpha
68 #else if str( $snp_options.select_model.model_type) == "snp": 67 #else if str( $snp_options.select_model.model_type) == "snp"
69 --model_type snp 68 --model_type snp
70 --alpha $snp_options.select_model.alpha 69 --alpha $snp_options.select_model.alpha
71 #else 70 #else
72 --model_type fixed 71 --model_type fixed
73 --bc_err_freq $bc_err_freq 72 --bc_err_freq $bc_err_freq
74 #end if 73 #end if
75 74
76 -o stacks_outputs 75 -o stacks_outputs
77 76
78 > ustacks.log 2>&1 77 2>&1 | tee ustacks.log
78
79 ## If input is in gz format, stacks will output gzipped files (no option to control this)
80 #if $sample.is_of_type('fastqsanger.gz')
81 && gunzip stacks_outputs/*.gz
82 #end if
83
84 &&
85
86 stacks_summary.py --stacks-prog ustacks --res-dir stacks_outputs --logfile ustacks.log --summary stacks_outputs/summary.html
79 ]]></command> 87 ]]></command>
80 88
81 <inputs> 89 <inputs>
82 <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" /> 90 <param name="sample" argument="-f" format="fastqsanger,fastqsanger.gz,fasta" type="data" label="Input short reads from an individual" />
83 91
84 <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/> 92 <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
85 <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> 93 <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
86 <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" /> 94 <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
87 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> 95 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
88 96
89 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True"> 97 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
90 <param name="r" argument="-r" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Enable the Removal algorithm, to drop highly-repetitive stacks (and nearby errors) from the algorithm" /> 98 <param name="keep_high_cov" argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep-high-cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. " />
91 <param name="d" argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" /> 99 <param name="d" argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" />
92 <param name="max_locus_stacks" argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/> 100 <param name="max_locus_stacks" argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
93 <param name="k_len" argument="--k_len" type="integer" value="" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/> 101 <param name="k_len" argument="--k_len" type="integer" value="" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
94 </section> 102 </section>
95 103
96 <conditional name="gapped"> 104 <conditional name="gapped">
97 <param name="use_gapped" argument="--gapped" type="boolean" checked="false" label="Perform gapped alignments between stacks" /> 105 <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">
98 <when value="false"></when> 106 <option value="no" selected="true">No</option>
99 <when value="true"> 107 <option value="yes">Yes</option>
108 </param>
109 <when value="no"/>
110 <when value="yes">
100 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/> 111 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
101 <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/> 112 <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
102 </when> 113 </when>
103 </conditional> 114 </conditional>
104 115
108 </section> 119 </section>
109 </inputs> 120 </inputs>
110 121
111 <outputs> 122 <outputs>
112 <data format="txt" name="output_log" label="ustacks.log with ${tool.name} on ${on_string}" from_work_dir="ustacks.log" /> 123 <data format="txt" name="output_log" label="ustacks.log with ${tool.name} on ${on_string}" from_work_dir="ustacks.log" />
124
125 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
113 126
114 <collection name="tabs" type="list" label="Stacks from ${on_string}"> 127 <collection name="tabs" type="list" label="Stacks from ${on_string}">
115 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> 128 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
116 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> 129 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
117 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> 130 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
126 <output name="output_log"> 139 <output name="output_log">
127 <assert_contents> 140 <assert_contents>
128 <has_text text="done." /> 141 <has_text text="done." />
129 </assert_contents> 142 </assert_contents>
130 </output> 143 </output>
144 <output name="output_summary">
145 <assert_contents>
146 <has_text text="Stacks Statistics" />
147 </assert_contents>
148 </output>
149
150 <output_collection name="tabs">
151 <element name="PopA_01.tags">
152 <assert_contents>
153 <has_text text="generated on " />
154 </assert_contents>
155 </element>
156 <element name="PopA_01.snps">
157 <assert_contents>
158 <has_text text="generated on " />
159 </assert_contents>
160 </element>
161 <element name="PopA_01.alleles">
162 <assert_contents>
163 <has_text text="generated on " />
164 </assert_contents>
165 </element>
166 <element name="PopA_01.models">
167 <assert_contents>
168 <has_text text="generated on " />
169 </assert_contents>
170 </element>
171 </output_collection>
172 </test>
173 <test>
174 <param name="sample" value="demultiplexed/PopA_01.1.fq.gzip" ftype="fastqsanger.gz" />
175
176 <output name="output_log">
177 <assert_contents>
178 <has_text text="done." />
179 </assert_contents>
180 </output>
181 <output name="output_summary">
182 <assert_contents>
183 <has_text text="Stacks Statistics" />
184 </assert_contents>
185 </output>
131 186
132 <output_collection name="tabs"> 187 <output_collection name="tabs">
133 <element name="PopA_01.tags"> 188 <element name="PopA_01.tags">
134 <assert_contents> 189 <assert_contents>
135 <has_text text="generated on " /> 190 <has_text text="generated on " />