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planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2
author cstrittmatter
date Fri, 12 Apr 2019 14:58:18 -0400
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children 1434bc7b4786
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1 <tool id="mitokmer_v1" name="mitokmer 1" version="1.0">
2 <description>Eukaryotic abundance prediction by mitochondrial content</description>
3 <requirements>
4 <requirement type="package" version="2.7">python</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 #if $reads.reads_select == "paired"
9 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
10 #set $forward = $reads.forward
11 #set $reverse = $reads.reverse
12 #else
13 #set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
14 #set $forward = $reads.allreads
15 #set $reverse = $reads.allreads
16 #end if
17 echo $name;
18 echo "-=-=-";
19 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
20 #set $fwd = "R1.fastq.gz"
21 #set $rev = "R2.fastq.gz"
22 #else if $forward.is_of_type('fastq', 'fastqsanger')
23 #set $fwd = "R1.fastq"
24 #set $rev = "R2.fastq"
25 #else if $forward.is_of_type('fasta.gz')
26 #set $fwd = "R1.fasta.gz"
27 #set $rev = "R2.fasta.gz"
28 #else
29 #set $fwd = "R1.fasta"
30 #set $rev = "R2.fasta"
31 #end if
32 ln -s $forward $fwd;
33 ln -s $reverse $rev;
34 #if $reads.reads_select == "single"
35 #set $rev = "none"
36 #end if
37 mkdir ./output;
38 python $__tool_directory__/kmer_read_m3.py
39 -w $__tool_directory__
40 -d ./output
41 -i $fwd $rev
42
43 ]]></command>
44 <inputs>
45
46 <conditional name="reads">
47 <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">
48 <option value="single">One FASTQ dataset from your history</option>
49 <option value="paired">Two FASTQ datasets from your history</option>
50 </param>
51 <when value="single">
52 <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
53 </when>
54 <when value="paired">
55 <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
56 <param label="Reverse reads" type="data" name="reverse" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
57 </when>
58 </conditional>
59
60 </inputs>
61 <outputs>
62 <data format="tabular" label="mitokmer Results" name="results" from_work_dir="output/mitokmer_result.csv"/>
63 </outputs>
64 <tests>
65 <test>
66 <param name="reads_select" value="single" />
67 <param name="allreads" value="1a.fasta" format="fasta"/>
68 <output name="output1" file="mitokmer_result.csv"/>
69 </test>
70 </tests>
71
72 <help><![CDATA[
73
74 **Usage: mitokmer.py**
75
76 ]]></help>
77 <citations>
78 <citation type="bibtex">
79 meh
80 }</citation>
81 </citations>
82
83 </tool>