Mercurial > repos > iuc > umi_tools_extract

comparison umi-tools_extract.xml @ 14:3b121a032e93 draft

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"planemo upload commit 59c614a9dda4b9f49bd3349fbde968ee5eca1db6"
author iuc
date Wed, 02 Jun 2021 18:22:53 +0000
parents faa2ba8e638d
children 343ca7cf18b2
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13:bd9ad5f9af98 14:3b121a032e93
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&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" /> 219 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{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