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comparison stacks_ustacks.xml @ 2:d033e1ccb386 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Thu, 16 Jul 2020 07:31:44 -0400
parents 21d2aa544835
children d1fda11e602f
comparison
equal deleted inserted replaced
1:21d2aa544835 2:d033e1ccb386
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @FASTQ_INPUT_FUNCTIONS@ 9 @FASTQ_INPUT_FUNCTIONS@
10 10
11 mkdir stacks_inputs stacks_outputs 11 trap ">&2 cat '$output_log'" err exit &&
12 12 mkdir stacks_inputs stacks_outputs &&
13 &&
14 13
15 #set $ID=1 14 #set $ID=1
16 #for $sample in $input_type.fqinputs 15 #for $sample in $input_type.fqinputs
17 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1") 16 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")
18 $create_links 17 $create_links
56 --model_type fixed 55 --model_type fixed
57 --bc_err_freq $bc_err_freq 56 --bc_err_freq $bc_err_freq
58 #end if 57 #end if
59 58
60 -o stacks_outputs 59 -o stacks_outputs
61
62 @TEE_APPEND_LOG@ 60 @TEE_APPEND_LOG@
61 &&
63 62
64 #set $ID=$ID+1 63 #set $ID=$ID+1
65 #end for 64 #end for
66 @CAT_LOG_TO_STDERR@ 65 true
67 ## If input is in gz format, stacks will output gzipped files (no option to control this) 66 ## If input is in gz format, stacks will output gzipped files (no option to control this)
68 #if $inputype.startswith('gz') 67 #if $inputype.startswith('gz')
69 && gunzip stacks_outputs/*.gz 68 && gunzip stacks_outputs/*.gz
70 #end if 69 #end if
71 ]]></command> 70 ]]></command>
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"/> 73 <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"/>
75 74
76 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/> 75 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/>
77 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> 76 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
78 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/> 77 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/>
79 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" /> 78 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads"/>
80 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> 79 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads"/>
81 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True"> 80 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
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. " /> 81 <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. "/>
83 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" /> 82 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags"/>
84 <param argument="--high_cov_thres" type="float" min="0.0" value="3.0" label="Highly-repetitive stacks threshold" help="in standard deviation units"/> 83 <param argument="--high_cov_thres" type="float" min="0.0" value="3.0" label="Highly-repetitive stacks threshold" help="in standard deviation units"/>
85 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/> 84 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
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)"/> 85 <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)"/>
87 </section> 86 </section>
88 <expand macro="gap_options"/> 87 <expand macro="gap_options"/>
99 <expand macro="ustacks_outputs_macro"/> 98 <expand macro="ustacks_outputs_macro"/>
100 </outputs> 99 </outputs>
101 100
102 <tests> 101 <tests>
103 <!-- paired list, default options, test for file equality --> 102 <!-- paired list, default options, test for file equality -->
104 <test> 103 <test expect_num_outputs="2">
105 <param name="input_type|input_type_select" value="paired"/> 104 <param name="input_type|input_type_select" value="paired"/>
106 <param name="input_type|fqinputs"> 105 <param name="input_type|fqinputs">
107 <collection type="list:paired"> 106 <collection type="list:paired">
108 <element name="PopA_01"> 107 <element name="PopA_01">
109 <collection type="paired"> 108 <collection type="paired">
110 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 109 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
111 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> 110 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
112 </collection> 111 </collection>
113 </element> 112 </element>
114 <element name="PopA_02"> 113 <element name="PopA_02">
115 <collection type="paired"> 114 <collection type="paired">
116 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> 115 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
117 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> 116 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
118 </collection> 117 </collection>
119 </element> 118 </element>
120 </collection> 119 </collection>
121 </param> 120 </param>
122 <param name="add_log" value="yes" /> 121 <param name="add_log" value="yes"/>
123 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> 122 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
123 <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version -->
124 <output_collection name="tabs" type="list" count="6"> 124 <output_collection name="tabs" type="list" count="6">
125 <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="4"/>
126 <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="4"/>
127 <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="4"/>
128 <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="4"/>
129 <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="4"/>
130 <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="4"/>
131 </output_collection> 131 </output_collection>
132 </test> 132 </test>
133 <!-- manual selected list of elements + default args, test for file equality --> 133 <!-- manual selected list of elements + default args, test for file equality -->
134 <test> 134 <test expect_num_outputs="2">
135 <param name="input_type|input_type_select" value="single"/> 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" /> 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" /> 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> 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"> 139 <output_collection name="tabs" count="6">
140 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 140 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
141 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 141 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
142 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 142 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
143 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> 143 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
144 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 144 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
145 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 145 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
146 </output_collection> 146 </output_collection>
147 </test> 147 </test>
148 <!-- 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 -->
149 <test> 149 <test expect_num_outputs="2">
150 <param name="input_type|input_type_select" value="single"/> 150 <param name="input_type|input_type_select" value="single"/>
151 <param name="input_type|fqinputs" 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"/>
152 <param name="m" value="2" /> 152 <param name="m" value="2"/>
153 <param name="M" value="3" /> 153 <param name="M" value="3"/>
154 <param name="N" value="4"/> 154 <param name="N" value="4"/>
155 <param name="R" value="-R" /> 155 <param name="R" value="-R"/>
156 <param name="H" value="-H" /> 156 <param name="H" value="-H"/>
157 <param name="add_log" value="yes" /> 157 <param name="add_log" value="yes"/>
158 <assert_command> 158 <assert_command>
159 <has_text text="-m 2" /> 159 <has_text text="-m 2"/>
160 <has_text text="-M 3" /> 160 <has_text text="-M 3"/>
161 <has_text text="-N 4" /> 161 <has_text text="-N 4"/>
162 <has_text text="-R" /> 162 <has_text text="-R"/>
163 <has_text text="-H" /> 163 <has_text text="-H"/>
164 </assert_command> 164 </assert_command>
165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> 165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
166 <output_collection name="tabs" count="6"> 166 <output_collection name="tabs" count="6">
167 <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="# ustacks completed on "/></assert_contents></element>
168 <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="# ustacks completed on "/></assert_contents></element>
169 <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="# ustacks completed on "/></assert_contents></element>
170 <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="# ustacks completed on "/></assert_contents></element>
171 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 171 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
172 <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="# ustacks completed on "/></assert_contents></element>
173 </output_collection> 173 </output_collection>
174 </test> 174 </test>
175 <!-- 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 -->
176 <test> 176 <test expect_num_outputs="2">
177 <param name="input_type|input_type_select" value="paired"/> 177 <param name="input_type|input_type_select" value="paired"/>
178 <param name="input_type|fqinputs"> 178 <param name="input_type|fqinputs">
179 <collection type="list:paired"> 179 <collection type="list:paired">
180 <element name="PopA_01"> 180 <element name="PopA_01">
181 <collection type="paired"> 181 <collection type="paired">
182 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 182 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
183 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> 183 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
184 </collection> 184 </collection>
185 </element> 185 </element>
186 <element name="PopA_02"> 186 <element name="PopA_02">
187 <collection type="paired"> 187 <collection type="paired">
188 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> 188 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
189 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> 189 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
190 </collection> 190 </collection>
191 </element> 191 </element>
192 </collection> 192 </collection>
193 </param> 193 </param>
196 <param name="alpha" value="0.1"/> 196 <param name="alpha" value="0.1"/>
197 <param name="bound_low" value="0.1"/> 197 <param name="bound_low" value="0.1"/>
198 <param name="bound_high" value="0.5"/> 198 <param name="bound_high" value="0.5"/>
199 <param name="bc_err_freq" value="0.1"/> 199 <param name="bc_err_freq" value="0.1"/>
200 </conditional> 200 </conditional>
201 <param name="gapped|use_gapped" value="no" /> 201 <param name="gapped|use_gapped" value="no"/>
202 <param name="add_log" value="yes" /> 202 <param name="add_log" value="yes"/>
203 <assert_command> 203 <assert_command>
204 <has_text text="--model_type snp" /> 204 <has_text text="--model_type snp"/>
205 <has_text text="--alpha 0.1" /> 205 <has_text text="--alpha 0.1"/>
206 <not_has_text text="--bound_low 0.1" /> 206 <not_has_text text="--bound_low 0.1"/>
207 <not_has_text text="--bound_high 0.5" /> 207 <not_has_text text="--bound_high 0.5"/>
208 <not_has_text text="--bc_err_freq 0.1" /> 208 <not_has_text text="--bc_err_freq 0.1"/>
209 <has_text text="--disable-gapped" /> 209 <has_text text="--disable-gapped"/>
210 </assert_command> 210 </assert_command>
211 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> 211 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
212 <output_collection name="tabs" count="6"> 212 <output_collection name="tabs" count="6">
213 <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="# ustacks completed on "/></assert_contents></element>
214 <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="# ustacks completed on "/></assert_contents></element>
215 <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="# ustacks completed on "/></assert_contents></element>
216 <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="# ustacks completed on "/></assert_contents></element>
217 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 217 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
218 <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="# ustacks completed on "/></assert_contents></element>
219 </output_collection> 219 </output_collection>
220 </test> 220 </test>
221 <!-- 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 -->
222 <test> 222 <test expect_num_outputs="2">
223 <param name="input_type|input_type_select" value="paired"/> 223 <param name="input_type|input_type_select" value="paired"/>
224 <param name="input_type|fqinputs"> 224 <param name="input_type|fqinputs">
225 <collection type="list"> 225 <collection type="list">
226 <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"/>
227 <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"/>
228 </collection> 228 </collection>
229 </param> 229 </param>
230 <param name="assembly_options|keep_high_cov" value="true"/> 230 <param name="assembly_options|keep_high_cov" value="true"/>
231 <param name="assembly_options|d" value="-d" /> 231 <param name="assembly_options|d" value="-d"/>
232 <param name="assembly_options|high_cov_thres" value="2.0"/> 232 <param name="assembly_options|high_cov_thres" value="2.0"/>
233 <param name="assembly_options|max_locus_stacks" value="4" /> 233 <param name="assembly_options|max_locus_stacks" value="4"/>
234 <param name="assembly_options|k_len" value="12"/> 234 <param name="assembly_options|k_len" value="12"/>
235 <param name="gapped|use_gapped" value="yes" /> 235 <param name="gapped|use_gapped" value="yes"/>
236 <param name="gapped|max_gaps" value="3" /> 236 <param name="gapped|max_gaps" value="3"/>
237 <param name="gapped|min_aln_len" value="0.7"/> 237 <param name="gapped|min_aln_len" value="0.7"/>
238 <param name="add_log" value="yes" /> 238 <param name="add_log" value="yes"/>
239 <assert_command> 239 <assert_command>
240 <has_text text="--keep_high_cov" /> 240 <has_text text="--keep_high_cov"/>
241 <has_text text="-d" /> 241 <has_text text="-d"/>
242 <has_text text="--high_cov_thres 2.0" /> 242 <has_text text="--high_cov_thres 2.0"/>
243 <has_text text="--max_locus_stacks 4" /> 243 <has_text text="--max_locus_stacks 4"/>
244 <has_text text="--k_len 12" /> 244 <has_text text="--k_len 12"/>
245 <has_text text="--max_gaps 3" /> 245 <has_text text="--max_gaps 3"/>
246 <has_text text="--min_aln_len 0.7" /> 246 <has_text text="--min_aln_len 0.7"/>
247 </assert_command> 247 </assert_command>
248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> 248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
249 <output_collection name="tabs" count="6"> 249 <output_collection name="tabs" count="6">
250 <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="# ustacks completed on "/></assert_contents></element>
251 <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="# ustacks completed on "/></assert_contents></element>
252 <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="# ustacks completed on "/></assert_contents></element>
253 <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="# ustacks completed on "/></assert_contents></element>
254 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> 254 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
255 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> 255 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
256 </output_collection> 256 </output_collection>
257 </test> 257 </test>
258 </tests> 258 </tests>
259 259
260 <help> 260 <help>
292 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 292 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
293 293
294 @STACKS_INFOS@ 294 @STACKS_INFOS@
295 ]]> 295 ]]>
296 </help> 296 </help>
297 <expand macro="citation" /> 297 <expand macro="citation"/>
298 </tool> 298 </tool>