Mercurial > repos > iuc > stacks2_procrad

comparison stacks_procrad.xml @ 2:bd5ff77e2036 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Wed, 15 Jul 2020 17:33:16 -0400
parents ca7aa77c7f57
children b4bab607eb05
comparison
equal deleted inserted replaced
1:ca7aa77c7f57 2:bd5ff77e2036
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="version_cmd"/> 8 <expand macro="version_cmd"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 @FASTQ_INPUT_FUNCTIONS@ 10 @FASTQ_INPUT_FUNCTIONS@
11
12 python '$__tool_directory__'/check_bcfile.py '$barcode' &&
13
11 mkdir stacks_inputs stacks_outputs && 14 mkdir stacks_inputs stacks_outputs &&
12 15
13 #if $output_log 16 #if $output_log
14 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && 17 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log &&
15 #end if 18 #end if
67 </when> 70 </when>
68 </conditional> 71 </conditional>
69 72
70 <section name="options_advanced" title="advanced options" expanded="False"> 73 <section name="options_advanced" title="advanced options" expanded="False">
71 <expand macro="common_advanced"/> 74 <expand macro="common_advanced"/>
72 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads" /> 75 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads"/>
73 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact" /> 76 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact"/>
74 <expand macro="rescue_barcode"/> 77 <expand macro="rescue_barcode"/>
75 <expand macro="process_adapter"/> 78 <expand macro="process_adapter"/>
76 </section> 79 </section>
77 80
78 <expand macro="process_filter"/> 81 <expand macro="process_filter"/>
84 <expand macro="out_log"/> 87 <expand macro="out_log"/>
85 <expand macro="process_outputs"/> 88 <expand macro="process_outputs"/>
86 </outputs> 89 </outputs>
87 <tests> 90 <tests>
88 <!-- single single ended input, no filtering (hence no capturing) + log --> 91 <!-- single single ended input, no filtering (hence no capturing) + log -->
89 <test> 92 <test expect_num_outputs="2">
90 <param name="input_type|input_type_select" value="single"/> 93 <param name="input_type|input_type_select" value="single"/>
91 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> 94 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
92 <param name="input_type|barcode_encoding" value="--inline_null"/> 95 <param name="input_type|barcode_encoding" value="--inline_null"/>
93 <param name="barcode" value="procrad/barcodes"/> 96 <param name="barcode" value="procrad/barcodes"/>
94 <param name="options_enzyme|options_enzyme_selector" value="1"/> 97 <param name="options_enzyme|options_enzyme_selector" value="1"/>
95 <param name="options_enzyme|enzyme" value="ecoRI"/> 98 <param name="options_enzyme|enzyme" value="ecoRI"/>
96 <param name="add_log" value="yes" /> 99 <param name="add_log" value="yes"/>
97 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/> 100 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/>
98 <output_collection name="demultiplexed" count="40"> 101 <output_collection name="demultiplexed" count="40">
99 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" /> 102 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger"/>
100 </output_collection> 103 </output_collection>
101 </test> 104 </test>
102 <!-- multiple (zipped) single end input (misusing R2 as add single end read file), 105 <!-- multiple (zipped) single end input (misusing R2 as add single end read file),
103 discarding by quality and capturing them --> 106 discarding by quality and capturing them -->
104 <test> 107 <test expect_num_outputs="3">
105 <param name="input_type|input_type_select" value="single"/> 108 <param name="input_type|input_type_select" value="single"/>
106 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/> 109 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/>
107 <param name="input_type|barcode_encoding" value="--inline_null"/> 110 <param name="input_type|barcode_encoding" value="--inline_null"/>
108 <param name="barcode" value="procrad/barcodes"/> 111 <param name="barcode" value="procrad/barcodes"/>
109 <param name="options_enzyme|options_enzyme_selector" value="1"/> 112 <param name="options_enzyme|options_enzyme_selector" value="1"/>
110 <param name="options_enzyme|enzyme" value="ecoRI"/> 113 <param name="options_enzyme|enzyme" value="ecoRI"/>
111 <param name="filter_cond|filter_select" value="yes"/> 114 <param name="filter_cond|filter_select" value="yes"/>
112 <param name="filter_cond|discard" value="-q"/> 115 <param name="filter_cond|discard" value="-q"/>
113 <param name="filter_cond|sliding" value="0.1" /> 116 <param name="filter_cond|sliding" value="0.1"/>
114 <param name="filter_cond|score" value="11" /> 117 <param name="filter_cond|score" value="11"/>
115 <param name="filter_cond|remove" value="-c" /> 118 <param name="filter_cond|remove" value="-c"/>
116 <param name="capture" value="-D"/> 119 <param name="capture" value="-D"/>
117 <param name="outype" value="gzfastq"/> 120 <param name="outype" value="gzfastq"/>
118 <param name="add_log" value="yes" /> 121 <param name="add_log" value="yes"/>
119 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> 122 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/>
120 <assert_command> 123 <assert_command>
121 <has_text text="-q" /> 124 <has_text text="-q"/>
122 <has_text text="-w 0.1" /> 125 <has_text text="-w 0.1"/>
123 <has_text text="-s 11" /> 126 <has_text text="-s 11"/>
124 <has_text text="-c" /> 127 <has_text text="-c"/>
125 <has_text text="-D" /> 128 <has_text text="-D"/>
126 </assert_command> 129 </assert_command>
127 <output_collection name="demultiplexed" count="40"> 130 <output_collection name="demultiplexed" count="40">
128 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> 131 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
129 </output_collection> 132 </output_collection>
130 <output_collection name="discarded" count="2"> 133 <output_collection name="discarded" count="2">
131 <element name="R1" file="procrad/R1.fq.discards" ftype="fastqsanger"/> 134 <element name="R1" file="procrad/R1.fq.discards" ftype="fastqsanger"/>
132 <element name="R2" file="procrad/R2.fq.discards" ftype="fastqsanger"/> 135 <element name="R2" file="procrad/R2.fq.discards" ftype="fastqsanger"/>
133 </output_collection> 136 </output_collection>
134 </test> 137 </test>
135 <!-- paired input, no quality but length filter, gzfasta output --> 138 <!-- paired input, no quality but length filter, gzfasta output -->
136 <test> 139 <test expect_num_outputs="4">
137 <param name="input_type|input_type_select" value="paired"/> 140 <param name="input_type|input_type_select" value="paired"/>
138 <param name="input_type|fqinputs"> 141 <param name="input_type|fqinputs">
139 <collection type="list:paired"> 142 <collection type="list:paired">
140 <element name="reads"> 143 <element name="reads">
141 <collection type="paired"> 144 <collection type="paired">
142 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" /> 145 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger"/>
143 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/> 146 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
144 </collection> 147 </collection>
145 </element> 148 </element>
146 </collection> 149 </collection>
147 </param> 150 </param>
150 <param name="options_enzyme|enzyme" value="ecoRI"/> 153 <param name="options_enzyme|enzyme" value="ecoRI"/>
151 <param name="filter_cond|filter_select" value="no"/> 154 <param name="filter_cond|filter_select" value="no"/>
152 <param name="filter_cond|len_limit" value="50"/> 155 <param name="filter_cond|len_limit" value="50"/>
153 <param name="capture" value="-D"/> 156 <param name="capture" value="-D"/>
154 <param name="outype" value="gzfasta"/> 157 <param name="outype" value="gzfasta"/>
155 <param name="add_log" value="yes" /> 158 <param name="add_log" value="yes"/>
156 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> 159 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/>
157 <assert_command> 160 <assert_command>
158 <has_text text="--len_limit 50" /> 161 <has_text text="--len_limit 50"/>
159 </assert_command> 162 </assert_command>
160 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> 163 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
161 <element name="PopA_01"> 164 <element name="PopA_01">
162 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz" /> 165 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz"/>
163 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz" /> 166 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz"/>
164 </element> 167 </element>
165 </output_collection> 168 </output_collection>
166 <output_collection name="remaining" type="list:paired" count="40"> 169 <output_collection name="remaining" type="list:paired" count="40">
167 <element name="PopA_01"> 170 <element name="PopA_01">
168 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/> 171 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/>
175 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/> 178 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/>
176 </element> 179 </element>
177 </output_collection> 180 </output_collection>
178 </test> 181 </test>
179 <!-- paired input (gzipped) + advanced options + two enzymes, fasta output --> 182 <!-- paired input (gzipped) + advanced options + two enzymes, fasta output -->
180 <test> 183 <test expect_num_outputs="3">
181 <param name="input_type|input_type_select" value="paired"/> 184 <param name="input_type|input_type_select" value="paired"/>
182 <param name="input_type|fqinputs"> 185 <param name="input_type|fqinputs">
183 <collection type="list:paired"> 186 <collection type="list:paired">
184 <element name="reads"> 187 <element name="reads">
185 <collection type="paired"> 188 <collection type="paired">
186 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz" /> 189 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/>
187 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> 190 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/>
188 </collection> 191 </collection>
189 </element> 192 </element>
190 </collection> 193 </collection>
191 </param> 194 </param>
192 <param name="barcode" value="procrad/barcodes"/> 195 <param name="barcode" value="procrad/barcodes"/>
193 <param name="options_enzyme|options_enzyme_selector" value="2"/> 196 <param name="options_enzyme|options_enzyme_selector" value="2"/>
194 <param name="options_enzyme|enzyme" value="ecoRI"/> 197 <param name="options_enzyme|enzyme" value="ecoRI"/>
195 <param name="options_enzyme|enzyme2" value="ecoRI"/> 198 <param name="options_enzyme|enzyme2" value="ecoRI"/>
196 <param name="options_advanced|truncate" value="70" /> 199 <param name="options_advanced|truncate" value="70"/>
197 <param name="options_advanced|rescue_cond|rescue" value="-r"/> 200 <param name="options_advanced|rescue_cond|rescue" value="-r"/>
198 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" /> 201 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2"/>
199 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" /> 202 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2"/>
200 <param name="options_advanced|bestrad" value="--bestrad" /> 203 <param name="options_advanced|bestrad" value="--bestrad"/>
201 <param name="options_advanced|retain_header" value="--retain_header"/> 204 <param name="options_advanced|retain_header" value="--retain_header"/>
202 <param name="options_advanced|disable_rad_check" value="--disable_rad_check" /> 205 <param name="options_advanced|disable_rad_check" value="--disable_rad_check"/>
203 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> 206 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/>
204 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> 207 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/>
205 <param name="options_advanced|adapter_mm" value="2" /> 208 <param name="options_advanced|adapter_mm" value="2"/>
206 <param name="outype" value="fasta"/> 209 <param name="outype" value="fasta"/>
207 <assert_command> 210 <assert_command>
208 <has_text text="-e ecoRI" /> 211 <has_text text="-e ecoRI"/>
209 <has_text text="--renz_2 ecoRI" /> 212 <has_text text="--renz_2 ecoRI"/>
210 <has_text text="-t 70" /> 213 <has_text text="-t 70"/>
211 <has_text text="-r" /> 214 <has_text text="-r"/>
212 <has_text text="--bestrad" /> 215 <has_text text="--bestrad"/>
213 <has_text text="--retain_header" /> 216 <has_text text="--retain_header"/>
214 <has_text text="--disable_rad_check" /> 217 <has_text text="--disable_rad_check"/>
215 <has_text text="--barcode_dist_1 2" /> 218 <has_text text="--barcode_dist_1 2"/>
216 <has_text text="--barcode_dist_2 2" /> 219 <has_text text="--barcode_dist_2 2"/>
217 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> 220 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/>
218 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> 221 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/>
219 <has_text text="--adapter_mm 2" /> 222 <has_text text="--adapter_mm 2"/>
220 </assert_command> 223 </assert_command>
221 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> 224 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
222 <element name="PopA_01"> 225 <element name="PopA_01">
223 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> 226 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/>
224 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/> 227 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/>
225 </element> 228 </element>
226 </output_collection> 229 </output_collection>
227 <output_collection name="remaining" type="list:paired" count="40"> 230 <output_collection name="remaining" type="list:paired" count="40">
228 <element name="PopA_01"> 231 <element name="PopA_01">
229 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta" /> 232 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta"/>
230 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta" /> 233 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta"/>
231 </element> 234 </element>
232 </output_collection> 235 </output_collection>
236 </test>
237 <!-- test invalid barcode file -->
238 <test expect_failure="true">
239 <param name="input_type|input_type_select" value="single"/>
240 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
241 <param name="input_type|barcode_encoding" value="--inline_null"/>
242 <param name="barcode" value="procrad/barcodes-duplicate"/>
243 <param name="options_enzyme|options_enzyme_selector" value="1"/>
244 <param name="options_enzyme|enzyme" value="ecoRI"/>
245 <param name="add_log" value="yes"/>
246 </test>
247 <!-- test invalid barcode file -->
248 <test expect_failure="true">
249 <param name="input_type|input_type_select" value="single"/>
250 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
251 <param name="input_type|barcode_encoding" value="--inline_null"/>
252 <param name="barcode" value="procrad/barcodes-duplicate2"/>
253 <param name="options_enzyme|options_enzyme_selector" value="1"/>
254 <param name="options_enzyme|enzyme" value="ecoRI"/>
255 <param name="add_log" value="yes"/>
256 </test>
257 <!-- test invalid barcode file -->
258 <test expect_failure="true">
259 <param name="input_type|input_type_select" value="single"/>
260 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
261 <param name="input_type|barcode_encoding" value="--inline_null"/>
262 <param name="barcode" value="procrad/barcodes-duplicate3"/>
263 <param name="options_enzyme|options_enzyme_selector" value="1"/>
264 <param name="options_enzyme|enzyme" value="ecoRI"/>
265 <param name="add_log" value="yes"/>
233 </test> 266 </test>
234 </tests> 267 </tests>
235
236 <help> 268 <help>
237 <![CDATA[ 269 <![CDATA[
238 .. class:: infomark 270 .. class:: infomark
239 271
240 **What it does** 272 **What it does**
288 The sample name column can be omitted. Then the Barcodes are used for naming the output files. 320 The sample name column can be omitted. Then the Barcodes are used for naming the output files.
289 321
290 @STACKS_INFOS@ 322 @STACKS_INFOS@
291 ]]> 323 ]]>
292 </help> 324 </help>
293 <expand macro="citation" /> 325 <expand macro="citation"/>
294 </tool> 326 </tool>