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comparison trimmomatic.xml @ 17:b9aaed85cbd1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit 6151dc895107d028c525362fb16b91388e10f2f2
author iuc
date Wed, 24 Jan 2024 08:56:01 +0000
parents 9a38087e3bfd
children
comparison
equal deleted inserted replaced
16:9a38087e3bfd 17:b9aaed85cbd1
118 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?"> 118 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
119 <option value="se" selected="true">Single-end</option> 119 <option value="se" selected="true">Single-end</option>
120 <option value="pair_of_files">Paired-end (two separate input files)</option> 120 <option value="pair_of_files">Paired-end (two separate input files)</option>
121 <option value="collection">Paired-end (as collection)</option> 121 <option value="collection">Paired-end (as collection)</option>
122 </param> 122 </param>
123 <when value="se"> 123 <when value="se">
124 <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" /> 124 <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
125 </when> 125 </when>
126 <when value="pair_of_files"> 126 <when value="pair_of_files">
127 <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" 127 <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
128 label="Input FASTQ file (R1/first of pair)" /> 128 label="Input FASTQ file (R1/first of pair)" />
129 <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" 129 <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
130 label="Input FASTQ file (R2/second of pair)" /> 130 label="Input FASTQ file (R2/second of pair)" />
131 </when> 131 </when>
132 <when value="collection"> 132 <when value="collection">
133 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" /> 133 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
134 </when> 134 </when>
135 </conditional> 135 </conditional>
136 <conditional name="illuminaclip"> 136 <conditional name="illuminaclip">
220 </param> 220 </param>
221 <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" /> 221 <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" />
222 <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" /> 222 <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" />
223 </inputs> 223 </inputs>
224 <outputs> 224 <outputs>
225 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in"> 225 <data name="fastq_out_r1_paired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
226 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> 226 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
227 </data> 227 </data>
228 <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in"> 228 <data name="fastq_out_r2_paired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
229 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> 229 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
230 </data> 230 </data>
231 <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in"> 231 <data name="fastq_out_r1_unpaired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
232 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> 232 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
233 </data> 233 </data>
234 <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in"> 234 <data name="fastq_out_r2_unpaired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
235 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> 235 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
236 </data> 236 </data>
237 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in"> 237 <data name="fastq_out" default_identifier_source="readtype|fastq_in" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
238 <filter>readtype['single_or_paired'] == 'se'</filter> 238 <filter>readtype['single_or_paired'] == 'se'</filter>
239 </data> 239 </data>
240 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired"> 240 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
241 <filter>readtype['single_or_paired'] == "collection"</filter> 241 <filter>readtype['single_or_paired'] == "collection"</filter>
242 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/> 242 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
243 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/> 243 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
244 </collection> 244 </collection>
245 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired"> 245 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
246 <filter>readtype['single_or_paired'] == "collection"</filter> 246 <filter>readtype['single_or_paired'] == "collection"</filter>
247 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> 247 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
248 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/> 248 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
249 </collection> 249 </collection>
250 <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog"> 250 <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
251 <filter>output_logs</filter> 251 <filter>output_logs</filter>
252 </data> 252 </data>
253 <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log"> 253 <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">