Mercurial > repos > iuc > umi_tools_extract

comparison umi-tools_extract.xml @ 21:158e9e91b9fc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e
author iuc
date Fri, 28 Feb 2025 20:41:17 +0000
parents 7a7e33d28f62
children
comparison
equal deleted inserted replaced
20:14ba4366aca4 21:158e9e91b9fc
81 #end if 81 #end if
82 #end if 82 #end if
83 ]]></command> 83 ]]></command>
84 <inputs> 84 <inputs>
85 <expand macro="input_types"> 85 <expand macro="input_types">
86 <param argument="--reconcile-pairs" type="boolean" truevalue="--reconcile-pairs" falsevalue="" checked="false" label="Allow unpaired reads" help="Allow the presences of reads in read2 input that are not present in read1 input. This allows cell barcode filtering of read1s without considering read2s" /> 86 <param argument="--reconcile-pairs" type="boolean" truevalue="--reconcile-pairs" falsevalue="" checked="false" label="Allow unpaired reads" help="Allow the presences of reads in read2 input that are not present in read1 input. This allows cell barcode filtering of read1s without considering read2s" />
87 </expand> 87 </expand>
88 <expand macro="fastq_barcode_extraction_options_macro"/> 88 <expand macro="fastq_barcode_extraction_options_macro"/>
89 89
90 <param argument="--whitelist" type="data" optional="true" format="txt,tabular,tsv" label="Allowlist of accepted barcodes" /> 90 <param argument="--whitelist" type="data" optional="true" format="txt,tabular,tsv" label="Allowlist of accepted barcodes" />
91 <param argument="--blacklist" type="data" optional="true" format="txt,tabular,tsv" label="Denylist of accepted barcodes" /> 91 <param argument="--blacklist" type="data" optional="true" format="txt,tabular,tsv" label="Denylist of accepted barcodes" />
132 <param name="bc_pattern" value="XXXNNN" /> 132 <param name="bc_pattern" value="XXXNNN" />
133 </conditional> 133 </conditional>
134 <conditional name="extract_method_cond"> 134 <conditional name="extract_method_cond">
135 <param name="prime3" value="true" /> 135 <param name="prime3" value="true" />
136 </conditional> 136 </conditional>
137 <param name="quality_selector" value="true" /> 137 <param name="quality|quality_selector" value="true" />
138 <param name="quality_filter_threshold" value="10" /> 138 <param name="quality|quality_filter_threshold" value="10" />
139 <param name="log" value="true"/> 139 <param name="log" value="true"/>
140 <output name="out" file="out_SE.fastq" ftype="fastqsanger" /> 140 <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
141 <output name="out_log" > 141 <output name="out_log" >
142 <assert_contents> 142 <assert_contents>
143 <has_text text="Input Reads: 100" /> 143 <has_text text="Input Reads: 100" />
164 </output> 164 </output>
165 </test> 165 </test>
166 <test expect_num_outputs="4"> 166 <test expect_num_outputs="4">
167 <conditional name="input_type_cond"> 167 <conditional name="input_type_cond">
168 <param name="input_type" value="paired_collection" /> <!-- same as before, but uncompressed --> 168 <param name="input_type" value="paired_collection" /> <!-- same as before, but uncompressed -->
169 <param name="paired_type" value="no" />
170 <param name="input_readpair"> 169 <param name="input_readpair">
171 <collection type="paired" > 170 <collection type="paired" >
172 <element name="forward" ftype="fastqsanger" value="t_R1.fastq" /> 171 <element name="forward" ftype="fastqsanger" value="t_R1.fastq" />
173 <element name="reverse" ftype="fastqsanger" value="t_R2.fastq" /> 172 <element name="reverse" ftype="fastqsanger" value="t_R2.fastq" />
174 </collection> 173 </collection>
192 <param name="input_type" value="paired" /> 191 <param name="input_type" value="paired" />
193 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastqsanger.gz" /> 192 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastqsanger.gz" />
194 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" /> 193 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
195 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" /> 194 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" />
196 </conditional> 195 </conditional>
197 <param name="extract_method" value="string" /> 196 <param name="extract_method_cond|extract_method" value="string" />
198 <param name="whitelist" value="scrb_seq_barcodes" /> 197 <param name="whitelist" value="scrb_seq_barcodes" />
199 <param name="log" value="true"/> 198 <param name="log" value="true"/>
200 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" /> 199 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" />
201 </test> 200 </test>
202 <test expect_num_outputs="3"><!-- same as above but with regex barcode--> 201 <test expect_num_outputs="3"><!-- same as above but with regex barcode-->
204 <param name="input_type" value="paired" /> 203 <param name="input_type" value="paired" />
205 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastqsanger.gz" /> 204 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastqsanger.gz" />
206 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" /> 205 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
207 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" /> 206 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" />
208 </conditional> 207 </conditional>
209 <param name="extract_method" value="regex" /> 208 <param name="extract_method_cond|extract_method" value="regex" />
210 <param name="whitelist" value="scrb_seq_barcodes" /> 209 <param name="whitelist" value="scrb_seq_barcodes" />
211 <param name="log" value="true"/> 210 <param name="log" value="true"/>
212 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" /> 211 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" />
213 </test> 212 </test>
214 <test expect_num_outputs="2"><!-- CelSeq2 example --> 213 <test expect_num_outputs="2"><!-- CelSeq2 example -->
216 <param name="input_type" value="paired" /> 215 <param name="input_type" value="paired" />
217 <param name="input_read1" value="read_R1.200.gz" ftype="fastqsanger.gz" /> 216 <param name="input_read1" value="read_R1.200.gz" ftype="fastqsanger.gz" />
218 <param name="input_read2" value="read_R2.200.gz" ftype="fastqsanger.gz" /> 217 <param name="input_read2" value="read_R2.200.gz" ftype="fastqsanger.gz" />
219 <param name="bc_pattern" value="NNNNNNCCCCCC" /> 218 <param name="bc_pattern" value="NNNNNNCCCCCC" />
220 </conditional> 219 </conditional>
221 <param name="extract_method" value="string" /> 220 <param name="extract_method_cond|extract_method" value="string" />
222 <output name="out" file="read_R1.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" /> 221 <output name="out" file="read_R1.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
223 <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" /> 222 <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
224 </test> 223 </test>
225 </tests> 224 </tests>
226 <help><![CDATA[ 225 <help><![CDATA[