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comparison mitokmer.1.xml @ 3:c9d98f5bc240 draft

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planemo upload commit 003cdb83fd17248ef57959332d58a3c96311332a-dirty
author cstrittmatter
date Sun, 28 Apr 2019 00:42:24 -0400
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2:a0852bb4b09b 3:c9d98f5bc240
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 rm $__tool_directory__/R*.fastq;
9 #if $reads.reads_select == "paired"
10 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
11 #set $forward = $reads.forward
12 #set $reverse = $reads.reverse
13 #else
14 #set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
15 #set $forward = $reads.allreads
16 #set $reverse = $reads.allreads
17 #end if
18 echo $name;
19 echo "-=-=-";
20 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
21 #set $fwd = "R1.fastq.gz"
22 #set $rev = "R2.fastq.gz"
23 #else if $forward.is_of_type('fastq', 'fastqsanger')
24 #set $fwd = "R1.fastq"
25 #set $rev = "R2.fastq"
26 #else if $forward.is_of_type('fasta.gz')
27 #set $fwd = "R1.fasta.gz"
28 #set $rev = "R2.fasta.gz"
29 #else
30 #set $fwd = "R1.fasta"
31 #set $rev = "R2.fasta"
32 #end if
33 ln -s $forward $__tool_directory__/$fwd;
34 ln -s $reverse $__tool_directory__/$rev;
35 #if $reads.reads_select == "single"
36 #set $rev = "none"
37 #end if
38 python $__tool_directory__/kmer_read_m3.py
39 -w $__tool_directory__
40 -d $__tool_directory__/output
41 -i $__tool_directory__/$fwd $__tool_directory__/$rev
42 ]]></command>
43 <inputs>
44
45 <conditional name="reads">
46 <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">
47 <option value="single">One FASTQ dataset from your history</option>
48 <option value="paired">Two FASTQ datasets from your history</option>
49 </param>
50 <when value="single">
51 <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
52 </when>
53 <when value="paired">
54 <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
55 <param label="Reverse reads" type="data" name="reverse" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
56 </when>
57 </conditional>
58
59 </inputs>
60 <outputs>
61 <data format="tabular" label="mitokmer Results" name="results" from_work_dir="output/mitokmer_result.csv"/>
62 </outputs>
63 <tests>
64 <test>
65 <param name="reads_select" value="single" />
66 <param name="allreads" value="1a.fasta" format="fasta"/>
67 <output name="output1" file="mitokmer_result.csv"/>
68 </test>
69 </tests>
70
71 <help><![CDATA[
72
73 **Usage: mitokmer.py**
74
75 ]]></help>
76 <citations>
77 <citation type="bibtex">
78 meh
79 }</citation>
80 </citations>
81
82 </tool>