Mercurial > repos > iuc > cawlign

annotate cawlign.xml @ 1:40ac05d4b9bc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 4d120e9ad135279a9159c65cdc2548a7e601b7cd
author iuc
date Mon, 08 Dec 2025 12:32:34 +0000
parents b304175b59ee
children
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b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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1 <tool id="cawlign" name="cawlign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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2 <description>Codon-aware (pairwise) alignment</description>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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3 <macros>
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4 <import>macros.xml</import>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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5 </macros>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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6 <expand macro="requirements"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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7 <expand macro="stdio"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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8 <command detect_errors="exit_code"><![CDATA[
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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9 cawlign
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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10 #if $reference_cond.reference_source == "history"
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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11 -r '$reference_cond.reference_history'
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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12 #else
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13 -r '$reference_cond.reference_builtin'
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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14 #end if
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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15 -s $scoring_matrix_cond.scoring_matrix_source.scoring_matrix
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16 -t $scoring_matrix_cond.datatype
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17 -l $local_alignment
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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18 -f $format
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19 -R $reverse_complement
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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20 $affine_gap
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21 $write_reference
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22 $fasta
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23 > '$output'
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24 ]]></command>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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25 <inputs>
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26 <param name="fasta" type="data" format="fasta" label="Sequences to align" help="Input FASTA file containing sequences to align."/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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27 <conditional name="reference_cond">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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28 <param name="reference_source" type="select" label="Reference sequence source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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29 <option value="builtin" selected="true">Use a built-in reference</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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30 <option value="history">Use a custom reference from history</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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31 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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32 <when value="builtin">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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33 <param name="reference_builtin" type="select" argument="-r" label="Select a built-in reference">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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34 <option value="CoV2-E">CoV2-E</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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35 <option value="CoV2-endornase">CoV2-endornase</option>
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36 <option value="CoV2-exonuclease">CoV2-exonuclease</option>
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37 <option value="CoV2-helicase">CoV2-helicase</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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38 <option value="CoV2-leader">CoV2-leader</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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39 <option value="CoV2-M">CoV2-M</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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40 <option value="CoV2-methyltransferase">CoV2-methyltransferase</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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41 <option value="CoV2-N">CoV2-N</option>
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42 <option value="CoV2-nsp10">CoV2-nsp10</option>
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43 <option value="CoV2-nsp2">CoV2-nsp2</option>
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44 <option value="CoV2-nsp3">CoV2-nsp3</option>
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45 <option value="CoV2-nsp4">CoV2-nsp4</option>
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46 <option value="CoV2-nsp6">CoV2-nsp6</option>
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47 <option value="CoV2-nsp7">CoV2-nsp7</option>
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48 <option value="CoV2-nsp8">CoV2-nsp8</option>
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49 <option value="CoV2-nsp9">CoV2-nsp9</option>
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50 <option value="CoV2-ORF10">CoV2-ORF10</option>
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51 <option value="CoV2-ORF1a">CoV2-ORF1a</option>
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52 <option value="CoV2-ORF1b">CoV2-ORF1b</option>
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53 <option value="CoV2-ORF3a">CoV2-ORF3a</option>
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54 <option value="CoV2-ORF5">CoV2-ORF5</option>
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55 <option value="CoV2-ORF6">CoV2-ORF6</option>
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56 <option value="CoV2-ORF7a">CoV2-ORF7a</option>
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57 <option value="CoV2-ORF7b">CoV2-ORF7b</option>
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58 <option value="CoV2-ORF8">CoV2-ORF8</option>
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59 <option value="CoV2-RdRp">CoV2-RdRp</option>
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60 <option value="CoV2-S">CoV2-S</option>
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61 <option value="CoV2-threeC">CoV2-threeC</option>
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62 <option value="HXB2_gag">HXB2_gag</option>
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63 <option value="HXB2_int">HXB2_int</option>
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64 <option value="HXB2_nef">HXB2_nef</option>
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65 <option value="HXB2_pol" selected="true">HXB2_pol</option>
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66 <option value="HXB2_pr">HXB2_pr</option>
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67 <option value="HXB2_prrt">HXB2_prrt</option>
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68 <option value="HXB2_rev">HXB2_rev</option>
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69 <option value="HXB2_rt">HXB2_rt</option>
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70 <option value="HXB2_tat">HXB2_tat</option>
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71 <option value="HXB2_vif">HXB2_vif</option>
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72 </param>
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73 </when>
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74 <when value="history">
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75 <param name="reference_history" type="data" argument="-r" format="fasta" label="Reference sequence" help="Reference sequence FASTA file from your history."/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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76 </when>
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77 </conditional>
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78 <conditional name="scoring_matrix_cond">
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79 <param name="datatype" type="select" argument="-t" label="Data type" help="Choose the alignment space (nucleotide, protein, or codon).">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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80 <option value="codon" selected="true">Align sequences in codon space</option>
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81 <option value="nucleotide">Align sequences in nucleotide space</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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82 <option value="protein">Align sequences in protein space</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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83 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
84 <when value="codon">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
85 <conditional name="scoring_matrix_source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
86 <param name="matrix_source" type="select" label="Scoring matrix source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
87 <option value="builtin" selected="true">Use a built-in scoring matrix</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
88 <option value="history">Use a custom scoring matrix from history</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
89 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
90 <when value="builtin">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
91 <param name="scoring_matrix" type="select" argument="-s" label="Scoring matrix" help="Select the scoring matrix to use.">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
92 <option value="BLOSUM62" selected="true">BLOSUM62 (for protein/codon alignments)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
93 <option value="HIV_BETWEEN_F">HIV_BETWEEN_F (for HIV alignments)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
94 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
95 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
96 <when value="history">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
97 <param name="scoring_matrix" type="data" argument="-s" format="tabular" label="Scoring matrix file" help="Scoring matrix file from your history. The file should be a tabular matrix with rows and columns representing amino acids or nucleotides, and cells containing substitution scores."/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
98 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
99 </conditional>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
100 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
101 <when value="nucleotide">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
102 <conditional name="scoring_matrix_source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
103 <param name="matrix_source" type="select" label="Scoring matrix source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
104 <option value="builtin" selected="true">Use a built-in scoring matrix</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
105 <option value="history">Use a custom scoring matrix from history</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
106 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
107 <when value="builtin">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
108 <param name="scoring_matrix" type="select" argument="-s" label="Scoring matrix" help="Select the scoring matrix to use.">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
109 <option value="NUC4.4" selected="true">NUC4.4 (for nucleotide alignments)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
110 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
111 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
112 <when value="history">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
113 <param name="scoring_matrix" type="data" argument="-s" format="tabular" label="Scoring matrix file" help="Scoring matrix file from your history. The file should be a tabular matrix with rows and columns representing amino acids or nucleotides, and cells containing substitution scores."/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
114 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
115 </conditional>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
116 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
117 <when value="protein">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
118 <conditional name="scoring_matrix_source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
119 <param name="matrix_source" type="select" label="Scoring matrix source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
120 <option value="history" selected="true">Use a custom scoring matrix from history</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
121 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
122 <when value="history">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
123 <param name="scoring_matrix" type="data" argument="-s" format="tabular" label="Scoring matrix file" help="Scoring matrix file from your history. The file should be a tabular matrix with rows and columns representing amino acids or nucleotides, and cells containing substitution scores."/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
124 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
125 </conditional>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
126 </when>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
127 </conditional>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
128 <param name="local_alignment" type="select" argument="-l" label="Global/local alignment" help="Select the alignment type.">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
129 <option value="trim" selected="true">Trim alignment (global to query, local to reference)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
130 <option value="global">Global alignment (all gaps scored equally)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
131 <option value="local">Local alignment (Smith-Waterman)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
132 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
133 <param name="format" type="select" argument="-f" label="Output format" help="Control the output format.">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
134 <option value="refmap" selected="true">Reference map (insertions not retained)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
135 <option value="refalign">Reference align (insertions retained)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
136 <option value="pairwise">Pairwise alignment (insertions retained, all pairwise alignments reported)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
137 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
138 <param name="reverse_complement" type="select" argument="-R" label="Reverse complementation" help="Handle reverse complementation.">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
139 <option value="none" selected="true">None</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
140 <option value="silent">Silent (try both strands, report best score)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
141 <option value="annotated">Annotated (like silent, but annotates strand)</option>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
142 </param>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
143 <param name="affine_gap" type="boolean" argument="-a" truevalue="-a" falsevalue="" checked="false" label="Disable affine gap scoring" help="Disable affine gap scoring (enabled by default)."/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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144 <param name="write_reference" type="boolean" argument="-I" truevalue="-I" falsevalue="" checked="false" label="Write out the reference sequence" help="Include the reference sequence in the output."/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
145 </inputs>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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diff changeset
146 <outputs>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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147 <data name="output" format="fasta" label="${tool.name} on ${on_string}: ${format}"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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148 </outputs>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
149 <tests>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
150 <test>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
151 <param name="fasta" value="OQ948666-pr-int-indel.fa" ftype="fasta"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
152 <conditional name="reference_cond">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
153 <param name="reference_source" value="builtin"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
154 <param name="reference_builtin" value="HXB2_pol"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
155 </conditional>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
156 <param name="format" value="refalign"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
157 <conditional name="scoring_matrix_cond">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
158 <param name="datatype" value="codon"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
159 <conditional name="scoring_matrix_source">
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
160 <param name="matrix_source" value="builtin"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
161 <param name="scoring_matrix" value="BLOSUM62"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
162 </conditional>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
163 </conditional>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
diff changeset
164 <output name="output" file="expected-result.fa" ftype="fasta"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
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165 </test>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
iuc
parents:
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166 </tests>
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iuc
parents:
diff changeset
167 <help><![CDATA[
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iuc
parents:
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168 .. class:: infomark
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169
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170 **What it does**
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171
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172 `cawlign` is a codon-aware aligner that maps sequences from a FASTA file to a reference sequence. It can perform nucleotide, protein, and codon-aware alignments.
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173
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174 **Input**
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175
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176 - **Sequences to align**: A FASTA file containing the sequences to be aligned.
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177 - **Reference sequence**: You can use a built-in reference sequence or provide one from your history.
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178 - **Scoring matrix**: You can use a built-in scoring matrix or provide one from your history. The available built-in matrices depend on the selected data type.
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179
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180 **Output**
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181
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182 A FASTA file containing the alignments. The structure of the output depends on the selected output format parameter (see Output Examples below).
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183
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184 .. class:: infomark
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185
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186 **Alignment Methods**
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187
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188 `cawlign` can perform three types of alignment: nucleotide, protein, and codon-aware.
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189
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190 * **Nucleotide Alignment**: This is a standard pairwise alignment of nucleotide sequences using the Smith-Waterman-Gotoh algorithm with affine gap penalties.
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191
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192 * **Protein Alignment**: This is a standard pairwise alignment of protein sequences, also using the Smith-Waterman-Gotoh algorithm with affine gap penalties. The nucleotide sequences are translated into amino acid sequences before alignment.
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193
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194 * **Codon-aware Alignment**: This is a more complex alignment method that is aware of the codon structure of the sequences. It aligns nucleotide sequences in codon space, which allows it to handle frameshift mutations (insertions or deletions that are not a multiple of 3 nucleotides) more accurately than a simple nucleotide alignment. This is achieved by using a dynamic programming algorithm that considers various types of codon matches and mismatches, including 3-to-1, 3-to-2, 3-to-4, and 3-to-5 matches. This makes it particularly useful for aligning coding sequences where frameshift mutations may have occurred, such as in viral genomes.
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195
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196 **Options**
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197
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198 - **Data type**: The type of alignment to perform.
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199 - **Nucleotide**: Align sequences in nucleotide space.
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200 - **Protein**: Align sequences in protein space.
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201 - **Codon**: Align sequences in codon space. This requires the reference to be in-frame.
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202
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203 - **Global/local alignment**: The type of alignment strategy.
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204 - **Trim**: A trimming alignment that is global with respect to the query and local with respect to the reference.
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205 - **Global**: Full string alignment; all gaps are scored equally.
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206 - **Local**: Partial string local (Smith-Waterman type) alignment that maximizes the alignment score.
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207
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208 - **Output format**: The format of the output file.
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209 - **Reference map**: Aligns query sequences to the reference and does not retain insertions relative to the reference.
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210 - **Reference align**: Aligns query sequences to the reference and does retain insertions relative to the reference. Insertions are shown in lowercase.
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211 - **Pairwise**: Aligns query sequences to the reference and does retain insertions relative to the reference; reports all pairwise alignments.
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212
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213 - **Reverse complementation**: How to handle reverse complementation.
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214 - **None**: No reverse complementation.
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215 - **Silent**: Try both forward and reverse-complemented query sequences and report the alignment with the best score.
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216 - **Annotated**: Like "Silent", but also annotates which strand was used.
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217
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218 - **Disable affine gap scoring**: By default, `cawlign` uses affine gap scoring. Check this option to disable it.
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219
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220 - **Write out the reference sequence**: Include the reference sequence in the output.
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221
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222 .. class:: infomark
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223
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224 **Output Examples**
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225
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226 Here are examples of what the different output formats look like using an example with an insertion ('gataca') and a deletion. The sequences are truncated for clarity.
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227
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228 **refmap**
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229
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230 The `refmap` output format aligns the query sequences to the reference but does not retain insertions relative to the reference.
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231
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232 .. code-block:: text
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233
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234 >OQ948666.1-indel
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235 CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACAATAAGGGTAGGGGGGCAATTAAAG...
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236
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237 **refalign**
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238
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239 The `refalign` output format also aligns the query sequences to the reference but *does* retain insertions, which are shown in lowercase.
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240
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241 .. code-block:: text
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242
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243 >OQ948666.1-indel
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244 CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACgatacaAATAAGGGTAGGGGGGCAATTAAAG...
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245
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246 **pairwise**
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247
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248 The `pairwise` output format reports the full pairwise alignment, including the reference sequence, with insertions and deletions shown as gaps in the corresponding sequence.
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249
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250 .. code-block:: text
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251
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252 >HXB2_pol
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253 CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCAC------AATAAAGATAGGGGGGCAACTAAAG...
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254 >OQ948666.1-indel
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255 CCTCAAATCACTCTTTGGCAGCGACCCATTGTCACGATACAAATAAGGGTAGGGGGGCAATTAAAG...
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256
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257 .. class:: infomalign
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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258
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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259 **References**
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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260
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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261 For more information, please visit the `cawlign` GitHub repository: https://github.com/veg/cawlign
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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262 ]]></help>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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263 <expand macro="citations"/>
b304175b59ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign commit 848922d15b3e17a864b3e40fdfed97e35f5646e5
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264 </tool>