Mercurial > repos > bgruening > nanopolish_eventalign

comparison nanopolish_eventalign.xml @ 6:855b7ba0ce9c draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4883f9a9a2779e2b4792314bd6128c7c109c00e1"
author bgruening
date Fri, 07 May 2021 06:49:26 +0000
parents 8fdb079ddaf0
children 3b6f94fc7e1d
comparison
equal deleted inserted replaced
5:8fdb079ddaf0 6:855b7ba0ce9c
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