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comparison seqkit_stats.xml @ 0:a40d1f17314e 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 05:37:21 +0000
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-1:000000000000 0:a40d1f17314e
1 <tool id="seqkit_stats" name="SeqKit statistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>of FASTA/Q files</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}' '${input_identifier}' &&
13
14 seqkit stats
15 '${input_identifier}'
16 $all
17 $basename
18 #if str($input.ext) in ['fastqsanger', 'fastqsanger.gz']:
19 --fq-encoding sanger
20 #end if
21 $skip_err
22 $tabular
23 > '$output'
24 ]]></command>
25 <inputs>
26 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
27 <param argument="--all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Output all statistics?" help="Includes quartiles of seq length, sum_gap, N50"/>
28 <param argument="--basename" type="boolean" truevalue="--basename" falsevalue="" checked="false" label="Output base name of input file?"/>
29 <param argument="--skip_err" type="boolean" truevalue="--skip-err" falsevalue="" checked="false" label="Skip errors?" help="Only show warning messages"/>
30 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" label="Output machine-friendly tabular format?"/>
31 </inputs>
32 <outputs>
33 <data name="output" format="txt">
34 <change_format>
35 <when input="tabular" value="--tabular" format="tabular"/>
36 </change_format>
37 </data>
38 </outputs>
39 <tests>
40 <test expect_num_outputs="1">
41 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
42 <param name="all" value="--all"/>
43 <output name="output" file="stats_output1.tabular" ftype="tabular"/>
44 </test>
45 <test expect_num_outputs="1">
46 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
47 <param name="all" value="--all"/>
48 <output name="output" file="stats_output2.tabular" ftype="tabular"/>
49 </test>
50 </tests>
51 <help>
52 **What it does**
53
54 Outputs simple statistics of FASTA/Q files; number of sequences, sum / min / avg / max sequence lengths, Q1, Q2, Q3,
55 sum gap, N50, Q20(%), and Q30(%).
56 </help>
57 <expand macro="citations"/>
58 </tool>
59