Mercurial > repos > thanhlv > polypolish
comparison polypolish.xml @ 3:5f21f2cf1ede draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit c28f9849db4c6c3e666447d28f61cf98329898ec-dirty"
| author | thanhlv |
|---|---|
| date | Fri, 23 Sep 2022 23:37:59 +0000 |
| parents | 96580cd76488 |
| children |
comparison
equal
deleted
inserted
replaced
| 2:96580cd76488 | 3:5f21f2cf1ede |
|---|---|
| 50 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> | 50 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> |
| 51 </when> | 51 </when> |
| 52 </conditional> | 52 </conditional> |
| 53 <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" /> | 53 <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" /> |
| 54 <param argument="fraction_invalid" type="float" value="0.2" min="0.0" max="1.0" label="Fraction value of the read depth to be considered invalid" /> | 54 <param argument="fraction_invalid" type="float" value="0.2" min="0.0" max="1.0" label="Fraction value of the read depth to be considered invalid" /> |
| 55 <param argument="fraction_valid" type="float" value="0.2" min="0.0" max="1.0" label="Ignore alignments with more than this many mismatches and indels" /> | 55 <param argument="fraction_valid" type="float" value="0.5" min="0.0" max="1.0" label="Ignore alignments with more than this many mismatches and indels" /> |
| 56 <param argument="max_errors" type="integer" value="10" min="1" label="Fraction value of the read depth to be considered invalid" /> | 56 <param argument="max_errors" type="integer" value="10" min="1" label="Fraction value of the read depth to be considered invalid" /> |
| 57 <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" /> | 57 <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" /> |
| 58 </inputs> | 58 </inputs> |
| 59 <outputs> | 59 <outputs> |
| 60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" /> | 60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" /> |
| 61 <data name="debug" format="tabular" from_work_dir="debug.tsv" label="${tool.name} on ${on_string} Polished assembly" > | 61 <data name="debug_tsv" format="tabular" from_work_dir="debug.tsv" label="${tool.name} on ${on_string} Polypolish debug" > |
| 62 <filter>debug is True</filter> | 62 <filter>debug is True</filter> |
| 63 </data> | 63 </data> |
| 64 </outputs> | 64 </outputs> |
| 65 <help><![CDATA[ | 65 <help><![CDATA[ |
| 66 ]]> </help> | 66 ]]> </help> |