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comparison seqtk_seq.xml @ 22:f2a792351212 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 09:08:17 +0000
parents 8f26884c60b6
children
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equal deleted inserted replaced
21:ac22e16bfecd 22:f2a792351212
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@.3"> 2 <tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@+galaxy1" profile="22.05">
3 <description>common transformation of FASTA/Q</description> 3 <description>common transformation of FASTA/Q</description>
4 <expand macro="bio_tools"/>
5 <macros> 4 <macros>
6 <import>macros.xml</import> 5 <import>macros.xml</import>
7 </macros> 6 </macros>
7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="stdio"/> 9 <expand macro="stdio"/>
10 <command><![CDATA[ 10 <command><![CDATA[
11 seqtk seq -q $q 11 seqtk seq -q $q
12 -X $X 12 -X $X
32 -V 32 -V
33 #end if 33 #end if
34 '$in_file' 34 '$in_file'
35 @CONDITIONAL_GZIP_OUT@ 35 @CONDITIONAL_GZIP_OUT@
36 ]]></command> 36 ]]></command>
37 <configfiles>
38 <configfile filename="outputs.json">
39 #if $A and $in_file.is_of_type('fasta.gz', 'fastq.gz')
40 #set $ext = "fasta.gz"
41 #elif $A
42 #set $ext = "fasta"
43 #else
44 #set $ext = $in_file.ext
45 #end if
46 {"default": {"ext": "$ext"}}
47 </configfile>
48 </configfiles>
37 <inputs> 49 <inputs>
38 <expand macro="in_faq"/> 50 <expand macro="in_faq"/>
39 <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" /> 51 <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" />
40 <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" /> 52 <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" />
41 <param argument="-n" type="text" value="0" label="Masked bases converted to CHAR; 0 for lowercase" /> 53 <param argument="-n" type="text" value="" label="Masked bases converted to CHAR; leave empty for lowercase masking" />
42 <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" /> 54 <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" />
43 <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" /> 55 <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" help="Only applied during comparison to quality thresholds for masking" />
44 <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" /> 56 <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" />
45 <param argument="-f" type="float" value="1" label="Sample fraction of sequences" /> 57 <param argument="-f" type="float" value="1" label="Sample fraction of sequences" />
46 <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" /> 58 <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" />
47 <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" /> 59 <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" />
48 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" /> 60 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" />
51 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" /> 63 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" />
52 <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" /> 64 <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
53 <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" /> 65 <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
54 <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" /> 66 <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
55 </inputs> 67 </inputs>
56 <outputs> 68 <outputs provided_metadata_file="outputs.json">
57 <data name="default" format_source="in_file" /> 69 <data name="default" format="auto" label="${tool.name} on ${on_string}" />
58 </outputs> 70 </outputs>
71
59 <tests> 72 <tests>
60 <!-- This is a sorry excuse for a test for a tool which does way more 73 <!-- This is a sorry excuse for a test for a tool which does way more
61 than it should, but upstream decided to put a TON of functionality 74 than it should, but upstream decided to put a TON of functionality
62 into a single tool rather than using the single responsibility 75 into a single tool rather than using the single responsibility
63 principle. --> 76 principle. -->
64 <test> 77 <test expect_num_outputs="1">
65 <param name="in_file" value="seqtk_seq.fa"/> 78 <param name="in_file" value="seqtk_seq.fa"/>
66 <param name="r" value="True"/> 79 <param name="r" value="True"/>
67 <param name="n" value=""/> 80 <param name="n" value=""/>
68 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/> 81 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
69 </test> 82 </test>
70 <test> 83 <test expect_num_outputs="1">
71 <param name="in_file" value="seqtk_seq.fa.gz" ftype="fasta.gz"/> 84 <param name="in_file" value="seqtk_seq.fa.gz" ftype="fasta.gz"/>
72 <param name="r" value="True"/> 85 <param name="r" value="True"/>
73 <param name="n" value=""/> 86 <param name="n" value=""/>
74 <output name="default" file="seqtk_seq_revcom.fa.gz" ftype="fasta.gz"/> 87 <output name="default" file="seqtk_seq_revcom.fa.gz" ftype="fasta.gz"/>
88 </test>
89 <test expect_num_outputs="1">
90 <param name="in_file" value="seqtk_trimfq.fq" ftype="fastq"/>
91 <param name="A" value="True" />
92 <output name="default" file="seqtk_seq_A.fasta" ftype="fasta"/>
93 </test>
94 <test expect_num_outputs="1">
95 <param name="in_file" value="seqtk_trimfq.fq.gz" ftype="fastq.gz"/>
96 <param name="A" value="True" />
97 <output name="default" file="seqtk_seq_A.fasta.gz" ftype="fasta.gz"/>
75 </test> 98 </test>
76 </tests> 99 </tests>
77 <help><![CDATA[ 100 <help><![CDATA[
78 **What it does** 101 **What it does**
79 102