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comparison 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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9:4b494533146a 10:a019807f4e67
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> 2 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@TOOL_VERSION@+galaxy1" profile="22.05">
3 <description>merge two FASTA/Q files</description> 3 <description>Merge two FASTA/Q files into a FASTA file output</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="bio_tools"/> 7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
16 $h 16 $h
17 '$in_fa1' 17 '$in_fa1'
18 '$in_fa2' 18 '$in_fa2'
19 #echo "| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default' 19 #echo "| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
20 ]]></command> 20 ]]></command>
21 <configfiles>
22 <configfile filename="outputs.json">
23 #set $ext = None
24 #if $in_fa1.is_of_type('fasta.gz', 'fastq.gz')
25 #set $ext = "fasta.gz"
26 #else
27 #set $ext = "fasta"
28 #end if
29 {"default": {"ext": "$ext"}}
30 </configfile>
31 </configfiles>
21 <inputs> 32 <inputs>
22 <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/> 33 <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
23 <param name="in_fa2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/> 34 <param name="in_fa2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
24 <param argument="-q" type="integer" value="0" label="Quality threshold"/> 35 <param argument="-q" type="integer" value="0" label="Quality threshold (for FASTQ)"/>
25 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" /> 36 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
26 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" /> 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." />
27 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" /> 38 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" />
28 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" /> 39 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" />
29 </inputs> 40 </inputs>
30 <outputs> 41 <outputs provided_metadata_file="outputs.json">
31 <data name="default" format_source="in_fa1" label="${tool.name} on ${on_string}"/> 42 <data name="default" format="auto" label="${tool.name} on ${on_string}" />
32 </outputs> 43 </outputs>
33 <tests> 44 <tests>
34 <test> 45 <test>
35 <param name="in_fa1" value="seqtk_mergefa1.fa"/> 46 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
36 <param name="in_fa2" value="seqtk_mergefa2.fa"/> 47 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
50 </test> 61 </test>
51 </tests> 62 </tests>
52 <help><![CDATA[ 63 <help><![CDATA[
53 **What it does** 64 **What it does**
54 65
55 Merges two fasta files, using ambiguity codes 66 This tool merges two FASTA or FASTQ files into a single FASTA file using IUPAC ambiguity codes where appropriate.
67 When differences occur between the sequences, ambiguity codes are used to represent possible variations.
56 68
57 :: 69 Example::
58 70
59 # seq1.fa 71 >seq1
60 >test0 72 ACTGACTGAAA
61 ACTGACTGAAA
62 73
63 # seq2.fa 74 >seq2
64 >test0 75 ACTGAMTGCGN
65 ACTGAMTGCGN
66 76
67 In the following the `-m` option has been set to highlight seqtk-mergefa's features. 77 will result in::
68 78
69 :: 79 >seq1
80 ACTGAMTGMRN
70 81
71 >test0 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.
72 ACTGACTGxxa 83 With this logic the input sequences above will result in the merge result::
84
85 >seq1
86 ACTGACTGxxa
73 87
74 @ATTRIBUTION@ 88 @ATTRIBUTION@
75 ]]></help> 89 ]]></help>
76 <expand macro="citation" /> 90 <expand macro="citation" />
77 </tool> 91 </tool>