annotate nextalign.xml @ 11:9ad6e80ea21f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit dd3394a10a05cf5d862222ef6a1e7edeaf150129"
author iuc
date Fri, 04 Feb 2022 21:25:49 +0000
parents 1c785a6b4d90
children 4d93e708218c
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1 <tool id="nextalign" name="NextAlign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Viral genome sequence alignment</description>
0
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3 <macros>
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4 <import>macros.xml</import>
6
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5 <token name="@VERSION_SUFFIX@">0</token>
0
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6 </macros>
2
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7 <requirements>
0
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8 <requirement type="package" version="@TOOL_VERSION@">nextalign</requirement>
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9 </requirements>
0
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10 <version_command>nextalign --version-detailed</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 @REF_FASTA@
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13 ln -s '$sequences' sequences.fasta &&
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14 nextalign
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15 --sequences sequences.fasta
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16 --reference reference.fa
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17 --output-fasta '$output_fasta'
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18 #if $output_insertions:
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19 --output-insertions '$output_csv'
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20 #end if
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21 #if $translation.translation_select == "yes":
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22 --genes '${translation.genes}'
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23 --genemap '${translation.genemap}'
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24 #end if
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25 --min-length '${min_length}'
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26 --penalty-gap-extend '${penalty_gap_extend}'
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27 --penalty-gap-open '${penalty_gap_open}'
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28 --penalty-gap-open-in-frame '${penalty_gap_open_in_frame}'
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29 --penalty-gap-open-out-of-frame '${penalty_gap_open_out_of_frame}'
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30 --penalty-mismatch '${penalty_mismatch}'
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31 --score-match '${score_match}'
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32 --max-indel '${max_indel}'
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33 --nuc-seed-length '${nuc_seed_length}'
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34 --nuc-min-seeds '${nuc_min_seeds}'
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35 --nuc-seed-spacing '${nuc_seed_spacing}'
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36 --nuc-mismatches-allowed '${nuc_mismatches_allowed}'
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37 ]]></command>
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38 <inputs>
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39 <expand macro="reference"/>
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40 <param argument="--sequences" type="data" format="fasta" label="FASTA file with input sequences"/>
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41 <param argument="--output-insertions" type="boolean" checked="true" label="Output insertion sequences?" help="Outputs stripped insertions relative to reference as CSV"/>
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42 <conditional name="translation">
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43 <param name="translation_select" type="select" label="Translate annotated genes based on GFF and gene list?">
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44 <option value="yes">Translate annotated genes</option>
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45 <option value="no">Don't translate genes</option>
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46 </param>
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47 <when value="yes">
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48 <param argument="--genes" type="text" label="Comma separated list of genes to translate.">
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49 <sanitizer invalid_char="">
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50 <valid initial="string.ascii_letters,string.digits">
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51 <add value="-" />
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52 <add value="." />
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53 <add value="," />
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54 </valid>
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55 </sanitizer>
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56 </param>
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57 <param argument="--genemap" type="data" format="gtf" label="GTF file containing custom gene map"/> <!-- TODO - make sure they need GFF and not GTF or GFF3 -->
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58 </when>
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59 <when value="no"/>
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60 </conditional>
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61 <param argument="--min-length" type="integer" value="100" min="0"
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62 label="Minimum length of nucleotide sequence to consider for alignment"
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63 help=" If a sequence is shorter than that, alignment will not be attempted and a warning will be emitted. When adjusting this parameter, note that alignment of short sequences can be unreliable." />
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64 <param argument="--penalty-gap-extend" type="integer" value="0"
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65 label="Penalty for extending a gap."
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66 help="If zero, all gaps regardless of length incur the same penalty." />
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67 <param argument="--penalty-gap-open" type="integer" value="6"
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68 label="Penalty for opening of a gap."
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69 help="A higher penalty results in fewer gaps and more mismatches. Should be less than the penalty value of opening a gap in frame to avoid gaps in genes." />
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70 <param argument="--penalty-gap-open-in-frame" type="integer" value="7" min="1"
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71 label="Penalty for opening gaps at the beginning of a codon."
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72 help="Should be greater than the penalty of opening a and less than penalty of opening a gap out of frame, to avoid gaps in genes, but favor gaps that align with codons." />
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73 <param argument="--penalty-gap-open-out-of-frame" type="integer" value="8" min="1"
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74 label="Penalty for opening gaps in the body of a codon."
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75 help="Should be greater than the penalty for opening gaps in-frame to favor gaps that align with codons." />
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76 <param argument="--penalty-mismatch" type="integer" value="1" min="1"
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77 label="Penalty for aligned nucleotides or aminoacids that differ in state during alignment"
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78 help="Note that this is redundantly parameterized with score match." />
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79 <param argument="--score-match" type="integer" value="3" min="1"
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80 label="Score for encouraging aligned nucelotides or aminoacids with matching state."
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81 help="Note that this is redundantly parameterized with mismatch penalty." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
82 <param argument="--max-indel" type="integer" value="400" min="0"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
83 label="Maximum length of insertions or deletions allowed to proceed with alignment."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
84 help="Alignments with long indels are slow to compute and require substantial memory in the current implementation. Alignment of sequences with indels that are longer than this value will not be attempted and a warning will be emitted." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
85 <param argument="--nuc-seed-length" type="integer" value="21" min="1"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
86 label="Seed length for nucleotide alignment."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
87 help="Seeds should be long enough to be unique, but short enough to match with high probability." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
88 <param argument="--nuc-min-seeds" type="integer" value="10" min="1"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
89 label="Minimum number of seeds to search for during nucleotide alignment."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
90 help="Relevant for short sequences. In long sequences, the number of seeds is determined by nucleotide seed spacing. This should be a positive integer." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
91 <param argument="--nuc-seed-spacing" type="integer" value="100" min="0"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
92 label="Spacing between seeds during nucleotide alignment." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
93 <param argument="--nuc-mismatches-allowed" type="integer" value="3" min="0"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
94 label="Maximum number of mismatching nucleotides."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
95 help="Maximum number of mismatching nucleotides allowed for a seed to be considered a match." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
96 </inputs>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
97 <outputs>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
98 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
99 <data name="output_csv" format="csv" label="${tool.name} on ${on_string} (CSV)">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
100 <filter>output_insertions</filter>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
101 </data>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
102 <collection name="translations" type="list" label="${tool.name} on ${on_string} - Translations (FASTA)">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
103 <discover_datasets pattern="sequences\.gene\.(?P&lt;designation&gt;[a-zA-Z0-9\-]+)\.fasta" format="fasta"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
104 <filter>translation['translation_select'] == 'yes'</filter>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
105 </collection>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
106 </outputs>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
107 <tests>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
108 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
109 Defaults, all outputs, reference from history
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
110 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
111 <test expect_num_outputs="3">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
112 <conditional name="reference_source">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
113 <param name="reference_source_selector" value="history"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
114 <param name="ref_file" value="reference.fasta"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
115 </conditional>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
116 <param name="output_insertions" value="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
117 <param name="sequences" value="subsampled.fasta"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
118 <conditional name="translation">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
119 <param name="translation_select" value="yes"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
120 <param name="genes" value="E,M,N,ORF10,ORF14,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
121 <param name="genemap" value="genemap.gtf" ftype="gtf"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
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diff changeset
122 </conditional>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
123 <output name="output_fasta" file="output.fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
124 <output name="output_csv" file="insertions.csv" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
125 <output_collection name="translations" type="list" count="14">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
126 <element name="E" file="subsampled.gene.E.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
127 <element name="M" file="subsampled.gene.M.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
128 <element name="N" file="subsampled.gene.N.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
129 <element name="ORF10" file="subsampled.gene.ORF10.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
130 <element name="ORF14" file="subsampled.gene.ORF14.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
131 <element name="ORF1a" file="subsampled.gene.ORF1a.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
132 <element name="ORF1b" file="subsampled.gene.ORF1b.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
133 <element name="ORF3a" file="subsampled.gene.ORF3a.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
134 <element name="ORF6" file="subsampled.gene.ORF6.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
135 <element name="ORF7a" file="subsampled.gene.ORF7a.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
136 <element name="ORF7b" file="subsampled.gene.ORF7b.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
137 <element name="ORF8" file="subsampled.gene.ORF8.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
138 <element name="ORF9b" file="subsampled.gene.ORF9b.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
139 <element name="S" file="subsampled.gene.S.fasta" ftype="fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
140 </output_collection>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
141 </test>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
142 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
143 Defaults, only fasta output, reference from history
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
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144 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
145 <test expect_num_outputs="1">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
146 <conditional name="reference_source">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
147 <param name="reference_source_selector" value="history"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
148 <param name="ref_file" value="reference.fasta"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
149 </conditional>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
150 <param name="output_insertions" value="false"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
151 <param name="sequences" value="subsampled.fasta"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
152 <conditional name="translation">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
153 <param name="translation_select" value="no"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
154 </conditional>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
155 <output name="output_fasta" file="output.fasta" sort="true"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
156 </test>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
157 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
158 Defaults, only fasta output, reference from cache
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
159 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
160 <test expect_num_outputs="1">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
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161 <conditional name="reference_source">
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162 <param name="reference_source_selector" value="cached"/>
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163 <param name="ref_file" value="reference_fasta"/>
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164 </conditional>
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165 <param name="output_insertions" value="false"/>
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166 <param name="sequences" value="subsampled.fasta"/>
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167 <conditional name="translation">
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168 <param name="translation_select" value="no"/>
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169 </conditional>
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170 <output name="output_fasta" file="output.fasta" sort="true"/>
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171 </test>
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172 </tests>
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173 <help><![CDATA[
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174
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175 **What it does**
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176
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177 Nextalign is a viral genome sequence alignment algorithm used in Nextclade.
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178
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179 It will perform a pairwise alignment of provided sequences against a given reference sequence using banded local alignment algorithm with
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180 affine gap-cost. Band width and rough relative positions are determined through seed matching.
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181
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182 Nextalign will strip insertions relative to the reference and output them in a separate CSV file.
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183
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184 Optionally, when provided with a gene map and a list of genes, Nextalign can perform translation of these genes.
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185
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186 Currently Nextalign primarily focuses on SARS-CoV-2 genome, but it can be used on any virus, given a sufficiently similar
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187 reference sequence (less than a 5% divergence).
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188
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189 ]]></help>
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190 <expand macro="citations" />
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191 </tool>