Mercurial > repos > iuc > seqtk

annotate seqtk_mergefa.xml @ 10:a019807f4e67 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
author iuc
date Wed, 16 Oct 2024 09:08:52 +0000
parents 4b494533146a
children
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@TOOL_VERSION@+galaxy1" profile="22.05">
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3 <description>Merge two FASTA/Q files into a FASTA file output</description>
3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 seqtk mergefa
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12 -q $q
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13 $i
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14 $m
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15 $r
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16 $h
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17 '$in_fa1'
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18 '$in_fa2'
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58c8ece95b53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 35c8480f525d211d5e9996086c60b2c6d4f89146"
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19 #echo "| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
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20 ]]></command>
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21 <configfiles>
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22 <configfile filename="outputs.json">
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23 #set $ext = None
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24 #if $in_fa1.is_of_type('fasta.gz', 'fastq.gz')
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25 #set $ext = "fasta.gz"
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26 #else
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27 #set $ext = "fasta"
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28 #end if
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29 {"default": {"ext": "$ext"}}
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30 </configfile>
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31 </configfiles>
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32 <inputs>
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33 <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
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34 <param name="in_fa2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
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35 <param argument="-q" type="integer" value="0" label="Quality threshold (for FASTQ)"/>
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36 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
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37 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Pick least ambiguous, mask conflicts and uncertainties" help="Tries to pick the least ambiguous symbol from the two inputs, but masks contradictory bases in the inputs as x in the merged result and converts the merged base to lowercase where one of the input bases is an N." />
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38 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" />
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39 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" />
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40 </inputs>
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41 <outputs provided_metadata_file="outputs.json">
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42 <data name="default" format="auto" label="${tool.name} on ${on_string}" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
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47 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
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48 <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
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49 </test>
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50 <test>
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51 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
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52 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
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53 <param name="m" value="True" />
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54 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
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55 </test>
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56 <test>
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57 <param name="in_fa1" value="seqtk_mergefa1.fa.gz" ftype="fasta.gz"/>
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58 <param name="in_fa2" value="seqtk_mergefa2.fa.gz" ftype="fasta.gz"/>
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59 <param name="m" value="True" />
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60 <output name="default" file="seqtk_mergefa2.out.gz" ftype="fasta.gz"/>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 **What it does**
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65
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66 This tool merges two FASTA or FASTQ files into a single FASTA file using IUPAC ambiguity codes where appropriate.
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67 When differences occur between the sequences, ambiguity codes are used to represent possible variations.
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68
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69 Example::
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70
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71 >seq1
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72 ACTGACTGAAA
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73
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74 >seq2
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75 ACTGAMTGCGN
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76
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77 will result in::
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78
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79 >seq1
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80 ACTGAMTGMRN
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81
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82 If the `-m` option is in use, however, the tool will pick the least ambiguous base if there is no contradiction between the symbols in the inputs. Conflicts are indicated by using x in the merged sequence and the picked base is converted to lowercase if the less specific symbol is an N to express uncertainty.
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83 With this logic the input sequences above will result in the merge result::
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84
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85 >seq1
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86 ACTGACTGxxa
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87
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88 @ATTRIBUTION@
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89 ]]></help>
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90 <expand macro="citation" />
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91 </tool>