comparison umi-tools_extract.xml @ 8:3cfd8e1073d7 draft

planemo upload commit f6178c9e071a2158a35b82a3607f6dc8a767675c
author iuc
date Mon, 16 Jul 2018 17:35:16 -0400
parents f77bc14eba31
children 828dba98cdb4
comparison
equal deleted inserted replaced
7:4756f7765416 8:3cfd8e1073d7
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&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" /> 238 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{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