Mercurial > repos > iuc > umi_tools_extract
comparison umi-tools_extract.xml @ 14:9fa7803d1c51 draft
"planemo upload commit 59c614a9dda4b9f49bd3349fbde968ee5eca1db6"
author | iuc |
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date | Wed, 02 Jun 2021 18:27:33 +0000 |
parents | d5ff68d2d5ff |
children | 27ac32a22ad2 |
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13:6a675c3aa610 | 14:9fa7803d1c51 |
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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"> | 5 <macro name="out_conditional"> |
6 <actions> | 6 <actions> |
66 --quality-filter-threshold '$quality.quality_filter_threshold' | 66 --quality-filter-threshold '$quality.quality_filter_threshold' |
67 --quality-encoding '$quality.quality_encoding' | 67 --quality-encoding '$quality.quality_encoding' |
68 #end if | 68 #end if |
69 #if $print_log == "1": | 69 #if $print_log == "1": |
70 --log='$out_log' | 70 --log='$out_log' |
71 #else | |
72 --supress-stats | |
73 #end if | 71 #end if |
74 #if $gz: | 72 #if $gz: |
75 #if $input_type.type == 'single': | 73 #if $input_type.type == 'single': |
76 && mv out.gz '$out' | 74 && mv out.gz '$out' |
77 #else | 75 #else |
151 <data name="out_log" format="txt"> | 149 <data name="out_log" format="txt"> |
152 <filter>print_log == True</filter> | 150 <filter>print_log == True</filter> |
153 </data> | 151 </data> |
154 </outputs> | 152 </outputs> |
155 <tests> | 153 <tests> |
156 <test> | 154 <test expect_num_outputs="2"> |
157 <param name="type" value="single" /> | 155 <param name="type" value="single" /> |
158 <param name="input_single" value="t_R1.fastq" ftype="fastq" /> | 156 <param name="input_single" value="t_R1.fastq" ftype="fastq" /> |
159 <param name="bc_pattern" value="XXXNNN" /> | 157 <param name="bc_pattern" value="XXXNNN" /> |
160 <param name="prime3" value="0" /> | 158 <param name="prime3" value="0" /> |
161 <param name="quality_selector" value="true" /> | 159 <param name="quality_selector" value="true" /> |
168 <has_text text="umi quality: 28" /> | 166 <has_text text="umi quality: 28" /> |
169 <has_text text="Reads output: 72" /> | 167 <has_text text="Reads output: 72" /> |
170 </assert_contents> | 168 </assert_contents> |
171 </output> | 169 </output> |
172 </test> | 170 </test> |
173 <test> | 171 <test expect_num_outputs="3"> |
174 <param name="type" value="paired" /> | 172 <param name="type" value="paired" /> |
175 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" /> | 173 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" /> |
176 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" /> | 174 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" /> |
177 <param name="bc_pattern" value="NNNXXX" /> | 175 <param name="bc_pattern" value="NNNXXX" /> |
178 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> | 176 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> |
182 <has_text text="Input Reads: 100" /> | 180 <has_text text="Input Reads: 100" /> |
183 <has_text text="Reads output: 100" /> | 181 <has_text text="Reads output: 100" /> |
184 </assert_contents> | 182 </assert_contents> |
185 </output> | 183 </output> |
186 </test> | 184 </test> |
187 <test> | 185 <test expect_num_outputs="3"> |
188 <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed --> | 186 <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed --> |
189 <param name="paired_type" value="no" /> | 187 <param name="paired_type" value="no" /> |
190 <param name="input_readpair" > | 188 <param name="input_readpair" > |
191 <collection type="paired" > | 189 <collection type="paired" > |
192 <element name="forward" ftype="fastq" value="t_R1.fastq" /> | 190 <element name="forward" ftype="fastq" value="t_R1.fastq" /> |
201 <has_text text="Input Reads: 100" /> | 199 <has_text text="Input Reads: 100" /> |
202 <has_text text="Reads output: 100" /> | 200 <has_text text="Reads output: 100" /> |
203 </assert_contents> | 201 </assert_contents> |
204 </output> | 202 </output> |
205 </test> | 203 </test> |
206 <test> | 204 <test expect_num_outputs="3"> |
207 <param name="type" value="paired" /> | 205 <param name="type" value="paired" /> |
208 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> | 206 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> |
209 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> | 207 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> |
210 <param name="extract_method" value="string" /> | 208 <param name="extract_method" value="string" /> |
211 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" /> | 209 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" /> |
212 <param name="use_barcodes" value="yes" /> | 210 <param name="use_barcodes" value="yes" /> |
213 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> | 211 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> |
214 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> | 212 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> |
215 </test> | 213 </test> |
216 <test><!-- same as above but with regex barcode--> | 214 <test expect_num_outputs="3"><!-- same as above but with regex barcode--> |
217 <param name="type" value="paired" /> | 215 <param name="type" value="paired" /> |
218 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> | 216 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" /> |
219 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> | 217 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" /> |
220 <param name="extract_method" value="regex" /> | 218 <param name="extract_method" value="regex" /> |
221 <param name="bc_pattern" value="^(?P<cell_1>.{6})(?P<umi_1>.{10})" /> | 219 <param name="bc_pattern" value="^(?P<cell_1>.{6})(?P<umi_1>.{10})" /> |
222 <param name="use_barcodes" value="yes" /> | 220 <param name="use_barcodes" value="yes" /> |
223 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> | 221 <param name="filter_barcode_file" value="scrb_seq_barcodes" /> |
224 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> | 222 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> |
225 </test> | 223 </test> |
226 <test><!-- CelSeq2 example --> | 224 <test expect_num_outputs="2"><!-- CelSeq2 example --> |
227 <param name="type" value="paired" /> | 225 <param name="type" value="paired" /> |
228 <param name="input_read1" value="read_R1.200.gz" ftype="fastq.gz" /> | 226 <param name="input_read1" value="read_R1.200.gz" ftype="fastq.gz" /> |
229 <param name="input_read2" value="read_R2.200.gz" ftype="fastq.gz" /> | 227 <param name="input_read2" value="read_R2.200.gz" ftype="fastq.gz" /> |
230 <param name="extract_method" value="string" /> | 228 <param name="extract_method" value="string" /> |
231 <param name="bc_pattern" value="NNNNNNCCCCCC" /> | 229 <param name="bc_pattern" value="NNNNNNCCCCCC" /> |
232 <output name="out1" file="read_R1.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> | 230 <output name="out1" file="read_R1.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> |
233 <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> | 231 <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" /> |
232 <param name="print_log" value="false"/> | |
234 </test> | 233 </test> |
235 </tests> | 234 </tests> |
236 <help><![CDATA[ | 235 <help><![CDATA[ |
237 | 236 |
238 | 237 |