Mercurial > repos > iuc > seqkit_stats
comparison seqkit_stats.xml @ 0:191738d53912 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
author | iuc |
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date | Wed, 01 Jun 2022 05:38:38 +0000 |
parents | |
children | 812705bcf39c |
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-1:000000000000 | 0:191738d53912 |
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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 |