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comparison nextalign.xml @ 8:d48000315087 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 017e25729a8ffd3722e87dfdf10ff4fd99c0babd"
author iuc
date Mon, 13 Dec 2021 17:01:14 +0000
parents ddf132c83068
children 8251e0ff00f8
comparison
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7:61e332ea171d 8:d48000315087
32 --max-indel '${max_indel}' 32 --max-indel '${max_indel}'
33 --nuc-seed-length '${nuc_seed_length}' 33 --nuc-seed-length '${nuc_seed_length}'
34 --nuc-min-seeds '${nuc_min_seeds}' 34 --nuc-min-seeds '${nuc_min_seeds}'
35 --nuc-seed-spacing '${nuc_seed_spacing}' 35 --nuc-seed-spacing '${nuc_seed_spacing}'
36 --nuc-mismatches-allowed '${nuc_mismatches_allowed}' 36 --nuc-mismatches-allowed '${nuc_mismatches_allowed}'
37 --aa-seed-length '${aa_seed_length}'
38 --aa-min-seeds '${aa_min_seeds}'
39 --aa-seed-spacing '${aa_seed_spacing}'
40 --aa-mismatches-allowed '${aa_mismatches_allowed}'
41 ]]></command> 37 ]]></command>
42 <inputs> 38 <inputs>
43 <expand macro="reference"/> 39 <expand macro="reference"/>
44 <param argument="--sequences" type="data" format="fasta" label="FASTA file with input sequences"/> 40 <param argument="--sequences" type="data" format="fasta" label="FASTA file with input sequences"/>
45 <param argument="--output-insertions" type="boolean" checked="true" label="Output insertion sequences?" help="Outputs stripped insertions relative to reference as CSV"/> 41 <param argument="--output-insertions" type="boolean" checked="true" label="Output insertion sequences?" help="Outputs stripped insertions relative to reference as CSV"/>
95 <param argument="--nuc-seed-spacing" type="integer" value="100" min="0" 91 <param argument="--nuc-seed-spacing" type="integer" value="100" min="0"
96 label="Spacing between seeds during nucleotide alignment." /> 92 label="Spacing between seeds during nucleotide alignment." />
97 <param argument="--nuc-mismatches-allowed" type="integer" value="3" min="0" 93 <param argument="--nuc-mismatches-allowed" type="integer" value="3" min="0"
98 label="Maximum number of mismatching nucleotides." 94 label="Maximum number of mismatching nucleotides."
99 help="Maximum number of mismatching nucleotides allowed for a seed to be considered a match." /> 95 help="Maximum number of mismatching nucleotides allowed for a seed to be considered a match." />
100 <param argument="--aa-seed-length" type="integer" value="12" min="1"
101 label="Seed length for aminoacid alignment" />
102 <param argument="--aa-min-seeds" type="integer" value="10" min="1"
103 label="Minimum number of seeds to search for during aminoacid alignment."
104 help="Relevant for short sequences. In long sequences, the number of seeds is determined by the aminoacid seed spacing." />
105 <param argument="--aa-seed-spacing" type="integer" value="100" min="0"
106 label="Spacing between seeds during aminoacid alignment." />
107 <param argument="--aa-mismatches-allowed" type="integer" value="2" min="0"
108 label="Maximum number of mismatching aminoacids."
109 help="Maximum number of mismatching aminoacids allowed for a seed to be considered a match." />
110 </inputs> 96 </inputs>
111 <outputs> 97 <outputs>
112 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/> 98 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
113 <data name="output_csv" format="csv" label="${tool.name} on ${on_string} (CSV)"> 99 <data name="output_csv" format="csv" label="${tool.name} on ${on_string} (CSV)">
114 <filter>output_insertions</filter> 100 <filter>output_insertions</filter>