Mercurial > repos > bgruening > nanopolish_eventalign
comparison nanopolish_eventalign.xml @ 10:d03669da4b59 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4883f9a9a2779e2b4792314bd6128c7c109c00e1"
| author | bgruening |
|---|---|
| date | Fri, 07 May 2021 06:46:05 +0000 |
| parents | 1286cea13ab0 |
| children |
comparison
equal
deleted
inserted
replaced
| 9:0ca2753c5090 | 10:d03669da4b59 |
|---|---|
| 1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy0"> | 1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy1"> |
| 2 <description>- Align nanopore events to reference k-mers</description> | 2 <description>- Align nanopore events to reference k-mers</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 47 -q $min_mapping_quality | 47 -q $min_mapping_quality |
| 48 #end if | 48 #end if |
| 49 --threads "\${GALAXY_SLOTS:-4}" | 49 --threads "\${GALAXY_SLOTS:-4}" |
| 50 $samples | 50 $samples |
| 51 $scale_events | 51 $scale_events |
| 52 $signal_index | |
| 52 $sam | 53 $sam |
| 53 $print_read_names | 54 $print_read_names |
| 54 #if $w and str($w).strip(): | 55 #if $w and str($w).strip(): |
| 55 -w "${w}" | 56 -w "${w}" |
| 56 #end if | 57 #end if |
| 108 label="Summarize the alignment of each read/strand" /> | 109 label="Summarize the alignment of each read/strand" /> |
| 109 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false" | 110 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false" |
| 110 label="Write the raw samples for the event to the tsv output" /> | 111 label="Write the raw samples for the event to the tsv output" /> |
| 111 <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" | 112 <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" |
| 112 label="Scale events to the model, rather than vice-versa" /> | 113 label="Scale events to the model, rather than vice-versa" /> |
| 114 <param name="signal_index" argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" | |
| 115 label="write the raw signal start and end index values for the event to the tsv output" /> | |
| 116 | |
| 117 | |
| 113 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" | 118 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" |
| 114 label="write output in SAM format" /> | 119 label="write output in SAM format" /> |
| 115 <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" | 120 <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" |
| 116 label="Print read names instead of indexes" /> | 121 label="Print read names instead of indexes" /> |
| 117 | 122 |