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comparison seqkit_fx2tab.xml @ 0:c1aa9a90b4c4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
author iuc
date Wed, 01 Jun 2022 05:39:05 +0000
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children 1dc73570fd5a
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-1:000000000000 0:c1aa9a90b4c4
1 <tool id="seqkit_fx2tab" name="SeqKit fx2tab" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>convert FASTA/Q to tabular</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10
11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
12 ln -s '${input}' '${input_identifier}' &&
13
14 seqkit fx2tab
15 '${input_identifier}'
16 $alphabet
17 $avg_qual
18 $gc
19 $gc_skew
20 $header_line
21 $length
22 $name
23 $no_qual
24 $only_id
25 #if str($input.ext) in ['fastqsanger', 'fastqsanger.gz']:
26 --qual-ascii-base 33
27 #end if
28 $seq_hash
29 > '$output'
30 ]]></command>
31 <inputs>
32 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
33 <param argument="--alphabet" type="boolean" truevalue="--alphabet" falsevalue="" checked="false" label="Output alphabet letters?"/>
34 <param argument="--avg_qual" type="boolean" truevalue="--avg-qual" falsevalue="" checked="false" label="Output average quality of the read?"/>
35 <param argument="--gc" type="boolean" truevalue="--gc" falsevalue="" checked="false" label="Output GC content?"/>
36 <param argument="--gc_skew" type="boolean" truevalue="--gc-skew" falsevalue="" checked="false" label="Output GC-Skew?"/>
37 <param argument="--header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="false" label="Output header line?"/>
38 <param argument="--length" type="boolean" truevalue="--length" falsevalue="" checked="false" label="Output sequence length?"/>
39 <param argument="--name" type="boolean" truevalue="--name" falsevalue="" checked="false" label="Output only names (no sequences and qualities)?"/>
40 <param argument="--no_qual" type="boolean" truevalue="--no-qual" falsevalue="" checked="false" label="Eliminate qualities from output?"/>
41 <param argument="--only_id" type="boolean" truevalue="--only-id" falsevalue="" checked="false" label="Output id instead of full head?"/>
42 <param argument="--seq_hash" type="boolean" truevalue="--seq-hash" falsevalue="" checked="false" label="Output md5 hash of sequence?"/>
43 </inputs>
44 <outputs>
45 <data name="output" format="tabular"/>
46 </outputs>
47 <tests>
48 <test expect_num_outputs="1">
49 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
50 <output name="output" file="fx2tab_output1.tabular" ftype="tabular"/>
51 </test>
52 <test expect_num_outputs="1">
53 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
54 <param name="avg_qual" value="--avg-qual"/>
55 <param name="header_line" value="--header-line"/>
56 <param name="length" value="--length"/>
57 <param name="name" value="--name"/>
58 <param name="only_id" value="--only-id"/>
59 <output name="output" file="fx2tab_output2.tabular" ftype="tabular"/>
60 </test>
61 <test expect_num_outputs="1">
62 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
63 <output name="output" file="fx2tab_output3.tabular" ftype="tabular"/>
64 </test>
65 <test expect_num_outputs="1">
66 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
67 <param name="alphabet" value="--alphabet"/>
68 <param name="avg_qual" value="--avg-qual"/>
69 <param name="gc" value="--gc"/>
70 <param name="gc_skew" value="--gc-skew"/>
71 <param name="header_line" value="--header-line"/>
72 <param name="length" value="--length"/>
73 <param name="name" value="--name"/>
74 <param name="no_qual" value="--no-qual"/>
75 <param name="only_id" value="--only-id"/>
76 <param name="seq_hash" value="--seq-hash"/>
77 <output name="output" file="fx2tab_output4.tabular" ftype="tabular"/>
78 </test>
79 </tests>
80 <help>
81 **What it does**
82
83 Converts FASTA/Q to tabular format and adds columns for sequence length and GC content/GC skew. The output
84 consists of 3 columns; id, sequence and quality unless one of the options to output only names or to eliminate
85 qualities is selected or additional columns (e.g., md5 sequence hash) are requested.
86 </help>
87 <expand macro="citations"/>
88 </tool>
89