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comparison stacks_ustacks.xml @ 5:ccbb048a4178 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
author matthias
date Wed, 27 Feb 2019 09:47:34 -0500
parents 784278062e27
children 742c94cfb8cf
comparison
equal deleted inserted replaced
4:adbf47759371 5:ccbb048a4178
1 <tool id="stacks2_ustacks" name="Stacks2: ustacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="stacks2_ustacks" name="Stacks2: ustacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>align short reads into stacks</description> 2 <description>Indentify unique stacks</description>
3 <macros> 3 <macros>
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="version_cmd"/>
8 <command><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @CLEAN_EXT@ 9 @FASTQ_INPUT_FUNCTIONS@
10 10
11 mkdir stacks_inputs stacks_outputs 11 mkdir stacks_inputs stacks_outputs
12 12
13 && 13 &&
14 14
15 #set $ID=1 15 #set $ID=1
16 #for $sample in $input_type.samples 16 #for $sample in $input_type.fqinputs
17 #set $read_direction="forward" 17 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")
18 @FASTQ_INPUT@ 18 $create_links
19 19
20 ustacks 20 ustacks
21 21
22 -f $data_path 22 -f '$data_path'
23 -i $ID 23 -i $ID
24 --name $name 24 --name $name
25 -m $m 25 -m $m
26 -M $M 26 -M $M
27 #if $N 27 #if $N
28 -N $N 28 -N $N
29 #end if 29 #end if
30 -p \${GALAXY_SLOTS:-1} 30 -p \${GALAXY_SLOTS:-1}
31 -t $inputype 31 -t $inputype
32 $R 32 $R
33 $H 33 $H
34 34
35 ## Assembly 35 ## Assembly
36 $assembly_options.keep_high_cov 36 $assembly_options.keep_high_cov
37 --high_cov_thres $assembly_options.high_cov_thres 37 --high_cov_thres $assembly_options.high_cov_thres
38 $assembly_options.d 38 $assembly_options.d
39 --max_locus_stacks $assembly_options.max_locus_stacks 39 --max_locus_stacks $assembly_options.max_locus_stacks
40 #if str($assembly_options.k_len) 40 #if str($assembly_options.k_len)
41 --k_len $assembly_options.k_len 41 --k_len $assembly_options.k_len
42 #end if 42 #end if
43 43
44 @GAP_OPTIONS@ 44 @GAP_OPTIONS@
45 45
46 ## snp_model 46 ## snp_model
47 #if str( $snp_options.select_model.model_type) == "bounded" 47 #if str( $snp_options.select_model.model_type) == "bounded"
48 --model_type bounded 48 --model_type bounded
49 --bound_low $snp_options.select_model.bound_low 49 --bound_low $snp_options.select_model.bound_low
50 --bound_high $snp_options.select_model.bound_high 50 --bound_high $snp_options.select_model.bound_high
54 --alpha $snp_options.select_model.alpha 54 --alpha $snp_options.select_model.alpha
55 #else 55 #else
56 --model_type fixed 56 --model_type fixed
57 --bc_err_freq $bc_err_freq 57 --bc_err_freq $bc_err_freq
58 #end if 58 #end if
59 59
60 -o stacks_outputs 60 -o stacks_outputs
61 61
62 @TEE_APPEND_LOG@ 62 @TEE_APPEND_LOG@
63 63
64 #set $ID=$ID+1 64 #set $ID=$ID+1
65 #end for 65 #end for
66 @CAT_LOG_TO_STDERR@ && 66 @CAT_LOG_TO_STDERR@
67 ## If input is in gz format, stacks will output gzipped files (no option to control this) 67 ## If input is in gz format, stacks will output gzipped files (no option to control this)
68 #if $inputype.startswith('gz') 68 #if $inputype.startswith('gz')
69 gunzip stacks_outputs/*.gz 69 && gunzip stacks_outputs/*.gz
70 #else
71 true
72 #end if 70 #end if
73 ]]></command> 71 ]]></command>
74 72
75 <inputs> 73 <inputs>
76 <expand macro="fastq_input_macro"/> 74 <expand macro="fastq_input" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"/>
77 75
78 <conditional name="input_type">
79 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks">
80 <option value="manual" selected="true">single end or forward reads</option>
81 <option value="list">(paired) data set list</option>
82 </param>
83 <when value="manual">
84 <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true"/>
85 </when>
86 <when value="list">
87 <param name="samples" argument="-f" type="data_collection" collection_type="list,list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs"/>
88 </when>
89 </conditional>
90 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/> 76 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/>
91 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> 77 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
92 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/> 78 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/>
93 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" /> 79 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
94 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> 80 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
95 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True"> 81 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
96 <param 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. " /> 82 <param 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. " />
97 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" /> 83 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" />
98 <param argument="--high_cov_thres" type="float" min="0.0" value="3.0" label="highly-repetitive stacks threshold" help="in standard deviation units"/> 84 <param argument="--high_cov_thres" type="float" min="0.0" value="3.0" label="Highly-repetitive stacks threshold" help="in standard deviation units"/>
99 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/> 85 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
100 <param argument="--k_len" type="integer" value="" min="7" max="31" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/> 86 <param argument="--k_len" type="integer" value="" min="7" max="31" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
101 </section> 87 </section>
102 <expand macro="gap_options"/> 88 <expand macro="gap_options"/>
103 89
112 <expand macro="out_log"/> 98 <expand macro="out_log"/>
113 <expand macro="ustacks_outputs_macro"/> 99 <expand macro="ustacks_outputs_macro"/>
114 </outputs> 100 </outputs>
115 101
116 <tests> 102 <tests>
117 <!-- manual selected list of elements + default args, test for file equality --> 103 <!-- paired list, default options, test for file equality -->
118 <test> 104 <test>
119 <param name="input_type|input_type_selector" value="manual"/> 105 <param name="input_type|input_type_select" value="paired"/>
120 <param name="input_type|samples" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> 106 <param name="input_type|fqinputs">
121 <param name="add_log" value="yes" /> 107 <collection type="list:paired">
122 <output name="output_log" ftype="txt" file="ustacks/ustacks.log" lines_diff="2"/> 108 <element name="PopA_01">
109 <collection type="paired">
110 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
111 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
112 </collection>
113 </element>
114 <element name="PopA_02">
115 <collection type="paired">
116 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
117 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
118 </collection>
119 </element>
120 </collection>
121 </param>
122 <param name="add_log" value="yes" />
123 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
123 <output_collection name="tabs" type="list" count="6"> 124 <output_collection name="tabs" type="list" count="6">
124 <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="2"/> 125 <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="2"/>
125 <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="2"/> 126 <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="2"/>
126 <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="2"/> 127 <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="2"/>
127 <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="2"/> 128 <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="2"/>
128 <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="2"/> 129 <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="2"/>
129 <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="2"/> 130 <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="2"/>
130 </output_collection> 131 </output_collection>
131 </test> 132 </test>
133 <!-- manual selected list of elements + default args, test for file equality -->
134 <test>
135 <param name="input_type|input_type_select" value="single"/>
136 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
137 <param name="add_log" value="yes" />
138 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
139 <output_collection name="tabs" count="6">
140 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
141 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
142 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
143 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
144 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
145 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
146 </output_collection>
147 </test>
132 <!-- manual selected list of elements + non-default short args, test for file presence --> 148 <!-- manual selected list of elements + non-default short args, test for file presence -->
133 <test> 149 <test>
134 <param name="input_type|input_type_selector" value="manual"/> 150 <param name="input_type|input_type_select" value="single"/>
135 <param name="input_type|samples" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> 151 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
136 <param name="-m" value="2" /> 152 <param name="-m" value="2" />
137 <param name="-M" value="3" /> 153 <param name="-M" value="3" />
138 <param name="-N" value="4"/> 154 <param name="-N" value="4"/>
139 <param name="-R" value="-R" /> 155 <param name="-R" value="-R" />
140 <param name="-H" value="-H" /> 156 <param name="-H" value="-H" />
144 <has_text text="-M 3" /> 160 <has_text text="-M 3" />
145 <has_text text="-N 5" /> 161 <has_text text="-N 5" />
146 <has_text text="-R" /> 162 <has_text text="-R" />
147 <has_text text="-H" /> 163 <has_text text="-H" />
148 </assert_command> 164 </assert_command>
149 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> 165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
150 <output_collection name="tabs" count="6"> 166 <output_collection name="tabs" count="6">
151 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 167 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
152 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 168 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
153 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 169 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
154 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 170 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
156 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 172 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
157 </output_collection> 173 </output_collection>
158 </test> 174 </test>
159 <!-- paired list, non-default model options, disabled gapped alignment, test for file presence --> 175 <!-- paired list, non-default model options, disabled gapped alignment, test for file presence -->
160 <test> 176 <test>
161 <param name="input_type|input_type_selector" value="list"/> 177 <param name="input_type|input_type_select" value="paired"/>
162 <param name="input_type|samples"> 178 <param name="input_type|fqinputs">
163 <collection type="list:paired"> 179 <collection type="list:paired">
164 <element name="PopA_01"> 180 <element name="PopA_01">
165 <collection type="paired"> 181 <collection type="paired">
166 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 182 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
167 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> 183 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
190 <has_text text="--bound_low 0.1" /> 206 <has_text text="--bound_low 0.1" />
191 <has_text text="--bound_high 0.5" /> 207 <has_text text="--bound_high 0.5" />
192 <has_text text="--bc_err_freq 0.1" /> 208 <has_text text="--bc_err_freq 0.1" />
193 <has_text text="--disable-gapped" /> 209 <has_text text="--disable-gapped" />
194 </assert_command> 210 </assert_command>
195 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> 211 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
196 <output_collection name="tabs" count="6"> 212 <output_collection name="tabs" count="6">
197 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 213 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
198 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 214 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
199 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 215 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
200 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 216 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
202 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 218 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
203 </output_collection> 219 </output_collection>
204 </test> 220 </test>
205 <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence --> 221 <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence -->
206 <test> 222 <test>
207 <param name="input_type|input_type_selector" value="list"/> 223 <param name="input_type|input_type_select" value="paired"/>
208 <param name="input_type|samples"> 224 <param name="input_type|fqinputs">
209 <collection type="list"> 225 <collection type="list">
210 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 226 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
211 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> 227 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
212 </collection> 228 </collection>
213 </param> 229 </param>
227 <has_text text="--max_locus_stacks 4" /> 243 <has_text text="--max_locus_stacks 4" />
228 <has_text text="--k_len 12" /> 244 <has_text text="--k_len 12" />
229 <has_text text="--max_gaps 3" /> 245 <has_text text="--max_gaps 3" />
230 <has_text text="--min_aln_len 3" /> 246 <has_text text="--min_aln_len 3" />
231 </assert_command> 247 </assert_command>
232 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> 248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
233 <output_collection name="tabs" count="6"> 249 <output_collection name="tabs" count="6">
234 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 250 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
235 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 251 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
236 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 252 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
237 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 253 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
251 267
252 -------- 268 --------
253 269
254 **Input files** 270 **Input files**
255 271
256 One or more FASTQ, FASTA files. Can be given by selecting them manually, as data set list, or paired data set list. Note, for the latter ustacks only uses the forward reads -- reverse reads are incorporated in tsv2bam. 272 One or more FASTQ, FASTA files. Can be given by selecting them manually, as dataset list, or paired dataset list. Note, for the latter ustacks only uses the forward reads -- reverse reads are incorporated in tsv2bam.
257 273
258 **Output files** 274 **Output files**
259 275
260 - XXX.tags.tsv file: 276 - XXX.tags.tsv file:
261 277