Mercurial > repos > iuc > nextalign

annotate nextalign.xml @ 0:d1dd7d1b07f6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
author iuc
date Thu, 08 Apr 2021 07:52:26 +0000
parents
children 74d1e42a87e0
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d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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1 <tool id="nextalign" name="NextAlign" version="@TOOL_VERSION@+galaxy0" profile="20.01">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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2 <macros>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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3 <import>macros.xml</import>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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4 </macros>
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5 <expand macro="requirements">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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6 <requirement type="package" version="@TOOL_VERSION@">nextalign</requirement>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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7 </expand>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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8 <version_command>nextalign --version-detailed</version_command>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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9 <command detect_errors="exit_code"><![CDATA[
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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10 @REF_FASTA@
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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11 ln -s '$sequences' sequences.fasta &&
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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12 nextalign
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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13 --sequences sequences.fasta
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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14 --reference reference.fa
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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15 --output-fasta '$output_fasta'
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16 #if $output_insertions:
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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17 --output-insertions '$output_csv'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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18 #end if
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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19 #if $translation.translation_select == "yes":
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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20 --genes '${translation.genes}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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21 --genemap '${translation.genemap}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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22 #end if
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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23 --min-length '${min_length}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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24 --penalty-gap-extend '${penalty_gap_extend}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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25 --penalty-gap-open '${penalty_gap_open}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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26 --penalty-gap-open-in-frame '${penalty_gap_open_in_frame}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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27 --penalty-gap-open-out-of-frame '${penalty_gap_open_out_of_frame}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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28 --penalty-mismatch '${penalty_mismatch}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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29 --score-match '${score_match}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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30 --max-indel '${max_indel}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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31 --nuc-seed-length '${nuc_seed_length}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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32 --nuc-min-seeds '${nuc_min_seeds}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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33 --nuc-seed-spacing '${nuc_seed_spacing}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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34 --nuc-mismatches-allowed '${nuc_mismatches_allowed}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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35 --aa-seed-length '${aa_seed_length}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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36 --aa-min-seeds '${aa_min_seeds}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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37 --aa-seed-spacing '${aa_seed_spacing}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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38 --aa-mismatches-allowed '${aa_mismatches_allowed}'
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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39 ]]></command>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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40 <inputs>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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41 <expand macro="reference"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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42 <param argument="--sequences" type="data" format="fasta" label="FASTA file with input sequences"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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43 <param argument="--output-insertions" type="boolean" checked="true" label="Output insertion sequences?" help="Outputs stripped insertions relative to reference as CSV"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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44 <conditional name="translation">
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45 <param name="translation_select" type="select" label="Translate annotated genes based on GFF and gene list?">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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46 <option value="yes">Translate annotated genes</option>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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47 <option value="no">Don't translate genes</option>
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48 </param>
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49 <when value="yes">
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50 <param argument="--genes" type="text" label="Comma separated list of genes to translate.">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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51 <sanitizer invalid_char="">
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52 <valid initial="string.ascii_letters,string.digits">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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53 <add value="-" />
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54 <add value="." />
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55 <add value="," />
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56 </valid>
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57 </sanitizer>
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58 </param>
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59 <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 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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60 </when>
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61 <when value="no"/>
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62 </conditional>
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63 <param argument="--min-length" type="integer" value="100" min="0"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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64 label="Minimum length of nucleotide sequence to consider for alignment"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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65 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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66 <param argument="--penalty-gap-extend" type="integer" value="0"
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67 label="Penalty for extending a gap."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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68 help="If zero, all gaps regardless of length incur the same penalty." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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69 <param argument="--penalty-gap-open" type="integer" value="6"
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70 label="Penalty for opening of a gap."
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71 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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72 <param argument="--penalty-gap-open-in-frame" type="integer" value="7" min="1"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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73 label="Penalty for opening gaps at the beginning of a codon."
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74 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." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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75 <param argument="--penalty-gap-open-out-of-frame" type="integer" value="8" min="1"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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76 label="Penalty for opening gaps in the body of a codon."
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77 help="Should be greater than the penalty for opening gaps in-frame to favor gaps that align with codons." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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78 <param argument="--penalty-mismatch" type="integer" value="1" min="1"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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79 label="Penalty for aligned nucleotides or aminoacids that differ in state during alignment"
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80 help="Note that this is redundantly parameterized with score match." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
81 <param argument="--score-match" type="integer" value="3" min="1"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
82 label="Score for encouraging aligned nucelotides or aminoacids with matching state."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
83 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
84 <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
85 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
86 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
87 <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
88 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
89 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
90 <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
91 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
92 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
93 <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
94 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
95 <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
96 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
97 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
98 <param argument="--aa-seed-length" type="integer" value="12" min="1"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
99 label="Seed length for aminoacid alignment" />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
100 <param argument="--aa-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
101 label="Minimum number of seeds to search for during aminoacid alignment."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
102 help="Relevant for short sequences. In long sequences, the number of seeds is determined by the aminoacid seed spacing." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
103 <param argument="--aa-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
104 label="Spacing between seeds during aminoacid alignment." />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
105 <param argument="--aa-mismatches-allowed" type="integer" value="2" min="0"
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
106 label="Maximum number of mismatching aminoacids."
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
107 help="Maximum number of mismatching aminoacids 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
108 </inputs>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
109 <outputs>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
110 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
111 <data name="output_csv" format="csv" label="${tool.name} on ${on_string} (CSV)">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
112 <filter>output_insertions</filter>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
113 </data>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
114 <collection name="translations" type="list" label="${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
115 <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
116 <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
117 </collection>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
118 </outputs>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
119 <tests>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
120 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
121 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
122 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
123 <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
124 <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
125 <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
126 <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
127 </conditional>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
128 <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
129 <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
130 <conditional name="translation">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
131 <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
132 <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
133 <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
parents:
diff changeset
134 </conditional>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
135 <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
136 <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
137 <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
138 <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
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 <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
146 <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
147 <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
148 <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
149 <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
150 <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
151 <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
152 </output_collection>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
153 </test>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
154 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
155 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:
diff changeset
156 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
157 <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
158 <conditional name="reference_source">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
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159 <param name="reference_source_selector" value="history"/>
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160 <param name="ref_file" value="reference.fasta"/>
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161 </conditional>
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162 <param name="output_insertions" value="false"/>
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163 <param name="sequences" value="subsampled.fasta"/>
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164 <conditional name="translation">
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165 <param name="translation_select" value="no"/>
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166 </conditional>
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167 <output name="output_fasta" file="output.fasta" sort="true"/>
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168 </test>
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169 <!--
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170 Defaults, only fasta output, reference from cache
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171 -->
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172 <test expect_num_outputs="1">
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173 <conditional name="reference_source">
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174 <param name="reference_source_selector" value="cached"/>
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175 <param name="ref_file" value="reference_fasta"/>
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176 </conditional>
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177 <param name="output_insertions" value="false"/>
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178 <param name="sequences" value="subsampled.fasta"/>
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179 <conditional name="translation">
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180 <param name="translation_select" value="no"/>
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181 </conditional>
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182 <output name="output_fasta" file="output.fasta" sort="true"/>
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183 </test>
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184 </tests>
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185 <help><![CDATA[
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186
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187 **What it does**
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188
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189 Nextalign is a viral genome sequence alignment algorithm used in Nextclade.
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190
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191 It will perform a pairwise alignment of provided sequences against a given reference sequence using banded local alignment algorithm with
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192 affine gap-cost. Band width and rough relative positions are determined through seed matching.
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193
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194 Nextalign will strip insertions relative to the reference and output them in a separate CSV file.
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195
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196 Optionally, when provided with a gene map and a list of genes, Nextalign can perform translation of these genes.
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197
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198 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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199 reference sequence (less than a 5% divergence).
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200
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201 ]]></help>
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202 <expand macro="citations" />
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203 </tool>