Mercurial > repos > frogs > frogs_core
comparison processing_short_reads_macros.xml @ 2:76ff9af5c0a3 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e987ae3594883fb3b12d2999c6ad7fccd0b1b64
| author | frogs |
|---|---|
| date | Fri, 06 Feb 2026 22:05:51 +0000 |
| parents | cd7675c5b15a |
| children |
comparison
equal
deleted
inserted
replaced
| 1:31abf44b6599 | 2:76ff9af5c0a3 |
|---|---|
| 116 <param argument="--input-R2" type="data" format="fastq" label="R2 reads (.fastq.gz)" help="R2 reads fastq file. Supported sequencers: Illumina and Aviti." /> | 116 <param argument="--input-R2" type="data" format="fastq" label="R2 reads (.fastq.gz)" help="R2 reads fastq file. Supported sequencers: Illumina and Aviti." /> |
| 117 </repeat> | 117 </repeat> |
| 118 </when> | 118 </when> |
| 119 </conditional> | 119 </conditional> |
| 120 <!-- Paired parameters --> | 120 <!-- Paired parameters --> |
| 121 <param argument="--R1-size" type="integer" label="R1 read length" help="Please provide the maximum length of the R1 reads." /> | 121 <param argument="--R1-size" value="300" type="integer" label="R1 read length" help="Please provide the maximum length of the R1 reads." /> |
| 122 <param argument="--R2-size" type="integer" label="R2 read length" help="Please provide the maximum length of the R2 reads." /> | 122 <param argument="--R2-size" value="300" type="integer" label="R2 read length" help="Please provide the maximum length of the R2 reads." /> |
| 123 <param argument="--mismatch-rate" type="float" value="0.1" label="Mismatch rate (used for R1-R2 merging)" help="Maximum allowed mismatch rate in the overlap region between R1 and R2 reads."/> | 123 <param argument="--mismatch-rate" type="float" value="0.1" label="Mismatch rate (used for R1-R2 merging)" help="Maximum allowed mismatch rate in the overlap region between R1 and R2 reads."/> |
| 124 <conditional name="merge_software_type"> | 124 <conditional name="merge_software_type"> |
| 125 <param argument="--merge-software" type="select" display="radio" label="Paired-end merging tool" help="Select the tool used to merge paired-end reads"> | 125 <param argument="--merge-software" type="select" display="radio" label="Paired-end merging tool" help="Select the tool used to merge paired-end reads"> |
| 126 <!-- <option value="pear" >Pear (only for non commercial, non military use. See Pear licence)</option> --> | 126 <!-- <option value="pear" >Pear (only for non commercial, non military use. See Pear licence)</option> --> |
| 127 <option value="vsearch" >Vsearch</option> | 127 <option value="vsearch" >Vsearch</option> |
| 128 <option value="flash">Flash</option> | 128 <option value="flash">Flash</option> |
| 129 </param> | 129 </param> |
| 130 <when value="vsearch"/> | 130 <when value="vsearch"/> |
| 131 <when value="flash"> | 131 <when value="flash"> |
| 132 <param argument="--expected-amplicon-size" type="integer" min="0" label="Expected amplicon length" help="Specify the maximum expected amplicon length (covers ~90% of amplicons)" /> | 132 <param argument="--expected-amplicon-size" type="integer" min="0" value="450" label="Expected amplicon length" help="Specify the maximum expected amplicon length (covers ~90% of amplicons)" /> |
| 133 </when> | 133 </when> |
| 134 </conditional> | 134 </conditional> |
| 135 <param argument="keep_unmerged" type="boolean" truevalue="--keep-unmerged" falsevalue="" checked="false" label="Would you like to keep unmerged reads?" help="No = unmerged reads will be removed; Yes = unmerged reads will be artificially combined with 100 N to allow further processing." /> | 135 <param argument="keep_unmerged" type="boolean" truevalue="--keep-unmerged" falsevalue="" checked="false" label="Would you like to keep unmerged reads?" help="No = unmerged reads will be removed; Yes = unmerged reads will be artificially combined with 100 N to allow further processing." /> |
| 136 </when> | 136 </when> |
| 137 <when value="single"> | 137 <when value="single"> |
| 154 </conditional> | 154 </conditional> |
| 155 </when> | 155 </when> |
| 156 </conditional> | 156 </conditional> |
| 157 | 157 |
| 158 <!-- Amplicons Parameters--> | 158 <!-- Amplicons Parameters--> |
| 159 <param argument="--min-amplicon-size" type="integer" value="" label="Minimum amplicon length" help="The minimum length of the amplicons (including primers). For paired-end reads, substract 10 bases to account for the minimum overlap between R1 and R2 reads."/> | 159 <param argument="--min-amplicon-size" type="integer" value="350" label="Minimum amplicon length" help="The minimum length of the amplicons (including primers). For paired-end reads, substract 10 bases to account for the minimum overlap between R1 and R2 reads."/> |
| 160 <param argument="--max-amplicon-size" type="integer" value="" label="Maximum amplicon length" help="The maximum length of the amplicons (including primers). For paired-end reads, substract 10 bases to account for the minimum overlap between R1 and R2 reads."/> | 160 <param argument="--max-amplicon-size" type="integer" value="500" label="Maximum amplicon length" help="The maximum length of the amplicons (including primers). For paired-end reads, substract 10 bases to account for the minimum overlap between R1 and R2 reads."/> |
| 161 | 161 |
| 162 <!-- Primers --> | 162 <!-- Primers --> |
| 163 <conditional name="is_primer_in_seq"> | 163 <conditional name="is_primer_in_seq"> |
| 164 <param name="primer_choice" type="select" display="radio" label="Do the sequences include PCR primers?" help="Indicate whether the sequences still include PCR primers. Select “Yes” if primers are present, “No” if they have already been removed." > | 164 <param name="primer_choice" type="select" display="radio" label="Do the sequences include PCR primers?" help="Indicate whether the sequences still include PCR primers. Select “Yes” if primers are present, “No” if they have already been removed." > |
| 165 <option value="true" selected="true">Yes</option> | 165 <option value="true" selected="true">Yes</option> |
| 166 <option value="false">No</option> | 166 <option value="false">No</option> |
| 167 </param> | 167 </param> |
| 168 <when value="true"> | 168 <when value="true"> |
| 169 <param argument="--five-prim-primer" type="text" label="5' primer" help="Enter the 5' primer sequence. Wildcards are allowed. The sequence must be provided in 5' → 3' orientation."> | 169 <param argument="--five-prim-primer" type="text" value="" optional="true" label="5' primer" help="Enter the 5' primer sequence. Wildcards are allowed. The sequence must be provided in 5' → 3' orientation."> |
| 170 <expand macro="only_letter_sanitizer_validator"/> | 170 <expand macro="only_letter_sanitizer_validator"/> |
| 171 </param> | 171 </param> |
| 172 <param argument="--three-prim-primer" type="text" label="3' primer" help="Enter the 3' primer sequence. Wildcards are allowed. The sequence must be provided in 5' → 3' orientation."> | 172 <param argument="--three-prim-primer" type="text" value="" optional="true" label="3' primer" help="Enter the 3' primer sequence. Wildcards are allowed. The sequence must be provided in 5' → 3' orientation."> |
| 173 <expand macro="only_letter_sanitizer_validator"/> | 173 <expand macro="only_letter_sanitizer_validator"/> |
| 174 </param> | 174 </param> |
| 175 </when> | 175 </when> |
| 176 <when value="false"/> | 176 <when value="false"/> |
| 177 </conditional> | 177 </conditional> |