Mercurial > repos > iuc > umi_tools_extract
comparison umi-tools_extract.xml @ 8:3cfd8e1073d7 draft
planemo upload commit f6178c9e071a2158a35b82a3607f6dc8a767675c
author | iuc |
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date | Mon, 16 Jul 2018 17:35:16 -0400 |
parents | f77bc14eba31 |
children | 828dba98cdb4 |
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7:4756f7765416 | 8:3cfd8e1073d7 |
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1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1"> | 1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.2"> |
2 <description>Extract UMI from fastq files</description> | 2 <description>Extract UMI from fastq files</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <macro name="out_conditional"> | |
6 <actions> | |
7 <conditional name="input_type.type"> | |
8 <when value="paired_collection" > | |
9 <action type="format"> | |
10 <option type="from_param" name="input_type.input_readpair" param_attribute="forward.ext" /> | |
11 </action> | |
12 </when> | |
13 <when value="paired" > | |
14 <action type="format"> | |
15 <option type="from_param" name="input_type.input_read1" param_attribute="ext" /> | |
16 </action> | |
17 </when> | |
18 </conditional> | |
19 </actions> | |
20 </macro> | |
5 </macros> | 21 </macros> |
6 <expand macro="requirements" /> | 22 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 23 <command detect_errors="exit_code"><![CDATA[ |
8 @COMMAND_LINK@ | 24 @COMMAND_LINK@ |
9 | 25 |
135 </param> | 151 </param> |
136 </when> | 152 </when> |
137 </conditional> | 153 </conditional> |
138 </inputs> | 154 </inputs> |
139 <outputs> | 155 <outputs> |
140 <data name="out" format_source="input_single"> | 156 <data name="out" format_source="input_single" label="Reads: ${tool.name} on ${on_string}" > |
141 <filter>input_type['type'] == "single"</filter> | 157 <filter>input_type['type'] == "single"</filter> |
142 </data> | 158 </data> |
143 <data name="out1" format_source="input_read1"> | 159 <data name="out1" format_source="input_read1" label="Reads1: ${tool.name} on ${on_string}" > |
144 <filter>input_type['type'] !== "single"</filter> | 160 <filter>input_type['type'] != "single"</filter> |
161 <expand macro="out_conditional" /> | |
145 </data> | 162 </data> |
146 <data name="out2" format_source="input_read2"> | 163 <data name="out2" format_source="input_read2" label="Reads2: ${tool.name} on ${on_string}" > |
147 <filter>input_type['type'] !== "single"</filter> | 164 <filter>input_type['type'] != "single"</filter> |
165 <expand macro="out_conditional" /> | |
148 </data> | 166 </data> |
167 | |
149 <data name="out_log" format="txt"> | 168 <data name="out_log" format="txt"> |
150 <filter>print_log == True</filter> | 169 <filter>print_log == True</filter> |
151 </data> | 170 </data> |
152 </outputs> | 171 </outputs> |
153 <tests> | 172 <tests> |
157 <param name="bc_pattern" value="XXXNNN" /> | 176 <param name="bc_pattern" value="XXXNNN" /> |
158 <param name="prime3" value="0" /> | 177 <param name="prime3" value="0" /> |
159 <param name="quality_selector" value="true" /> | 178 <param name="quality_selector" value="true" /> |
160 <param name="quality_filter_threshold" value="10" /> | 179 <param name="quality_filter_threshold" value="10" /> |
161 <param name="quality_encoding" value="phred33" /> | 180 <param name="quality_encoding" value="phred33" /> |
162 <output name="out" file="out_SE.fastq" /> | 181 <output name="out" file="out_SE.fastq" ftype="fastq" /> |
163 <output name="out_log" file="out_single.log" lines_diff="22"/> | 182 <output name="out_log" > |
183 <assert_contents> | |
184 <has_text text="Input Reads: 100" /> | |
185 <has_text text="umi quality: 28" /> | |
186 <has_text text="Reads output: 72" /> | |
187 </assert_contents> | |
188 </output> | |
164 </test> | 189 </test> |
165 <test> | 190 <test> |
166 <param name="type" value="paired" /> | 191 <param name="type" value="paired" /> |
167 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" /> | 192 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" /> |
168 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" /> | 193 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" /> |
169 <param name="bc_pattern" value="NNNXXX" /> | 194 <param name="bc_pattern" value="NNNXXX" /> |
170 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> | 195 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> |
171 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> | 196 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> |
172 <output name="out_log" file="out_paired.log" lines_diff="16"/> | 197 <output name="out_log" > |
198 <assert_contents> | |
199 <has_text text="Input Reads: 100" /> | |
200 <has_text text="Reads output: 100" /> | |
201 </assert_contents> | |
202 </output> | |
173 </test> | 203 </test> |
174 <test> | 204 <test> |
175 <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed --> | 205 <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed --> |
206 <param name="paired_type" value="no" /> | |
176 <param name="input_readpair" > | 207 <param name="input_readpair" > |
177 <collection type="paired"> | 208 <collection type="paired" > |
178 <element name="forward" ftype="fastq" value="t_R1.fastq" /> | 209 <element name="forward" ftype="fastq" value="t_R1.fastq" /> |
179 <element name="reverse" ftype="fastq" value="t_R2.fastq" /> | 210 <element name="reverse" ftype="fastq" value="t_R2.fastq" /> |
180 </collection> | 211 </collection> |
181 </param> | 212 </param> |
182 <param name="bc_pattern" value="NNNXXX" /> | 213 <param name="bc_pattern" value="NNNXXX" /> |
183 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> | 214 <output name="out1" file="out_R1.fastq" ftype="fastq" /> |
184 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> | 215 <output name="out2" file="out_R2.fastq" ftype="fastq" /> |
185 <output name="out_log" file="out_paired.log" lines_diff="25" /> | 216 <output name="out_log" > |
217 <assert_contents> | |
218 <has_text text="Input Reads: 100" /> | |
219 <has_text text="Reads output: 100" /> | |
220 </assert_contents> | |
221 </output> | |
186 </test> | 222 </test> |
187 <test> | 223 <test> |
188 <param name="type" value="paired" /> | 224 <param name="type" value="paired" /> |
189 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> | 225 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> |
190 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> | 226 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> |
191 <param name="extract_method" value="string" /> | 227 <param name="extract_method" value="string" /> |
192 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" /> | 228 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" /> |
193 <param name="use_barcodes" value="yes" /> | 229 <param name="use_barcodes" value="yes" /> |
194 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> | 230 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> |
195 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" /> | 231 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> |
196 </test> | 232 </test> |
197 <test><!-- same as above but with regex barcode--> | 233 <test><!-- same as above but with regex barcode--> |
198 <param name="type" value="paired" /> | 234 <param name="type" value="paired" /> |
199 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> | 235 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> |
200 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> | 236 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> |
201 <param name="extract_method" value="regex" /> | 237 <param name="extract_method" value="regex" /> |
202 <param name="bc_pattern" value="^(?P<cell_1>.{6})(?P<umi_1>.{10})" /> | 238 <param name="bc_pattern" value="^(?P<cell_1>.{6})(?P<umi_1>.{10})" /> |
203 <param name="use_barcodes" value="yes" /> | 239 <param name="use_barcodes" value="yes" /> |
204 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> | 240 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> |
205 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" /> | 241 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> |
242 </test> | |
243 <test><!-- CelSeq2 example --> | |
244 <param name="type" value="paired" /> | |
245 <param name="input_read1" value="read_R1.200.gz" ftype="fastq.gz" /> | |
246 <param name="input_read2" value="read_R2.200.gz" ftype="fastq.gz" /> | |
247 <param name="extract_method" value="string" /> | |
248 <param name="bc_pattern" value="NNNNNNCCCCCC" /> | |
249 <output name="out1" file="read_R1.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> | |
250 <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> | |
206 </test> | 251 </test> |
207 </tests> | 252 </tests> |
208 <help><![CDATA[ | 253 <help><![CDATA[ |
209 | 254 |
210 | 255 |