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comparison mitokmer.xml @ 2:a0852bb4b09b draft

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planemo upload commit 03463f4b0598df5619def5230de3fb758b4090ba-dirty
author cstrittmatter
date Thu, 25 Apr 2019 07:59:05 -0400
parents 1434bc7b4786
children c9d98f5bc240
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1:1434bc7b4786 2:a0852bb4b09b
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 7
8 #if $reads.reads_select == "paired" 8 rm $__tool_directory__/R*.fastq;
9 #set $name = $reads.forward.name.split('.')[0].replace(' ','_') 9 #if $reads.reads_select == "paired"
10 #set $forward = $reads.forward 10 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
11 #set $reverse = $reads.reverse 11 #set $forward = $reads.forward
12 #else 12 #set $reverse = $reads.reverse
13 #set $name = $reads.allreads.name.split('.')[0].replace(' ','_') 13 #else
14 #set $forward = $reads.allreads 14 #set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
15 #set $reverse = $reads.allreads 15 #set $forward = $reads.allreads
16 #end if 16 #set $reverse = $reads.allreads
17 #end if
17 echo $name; 18 echo $name;
18 echo "-=-=-"; 19 echo "-=-=-";
19 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz') 20 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
20 #set $fwd = "R1.fastq.gz" 21 #set $fwd = "R1.fastq.gz"
21 #set $rev = "R2.fastq.gz" 22 #set $rev = "R2.fastq.gz"
22 #else if $forward.is_of_type('fastq', 'fastqsanger') 23 #else if $forward.is_of_type('fastq', 'fastqsanger')
23 #set $fwd = "R1.fastq" 24 #set $fwd = "R1.fastq"
24 #set $rev = "R2.fastq" 25 #set $rev = "R2.fastq"
25 #else if $forward.is_of_type('fasta.gz') 26 #else if $forward.is_of_type('fasta.gz')
26 #set $fwd = "R1.fasta.gz" 27 #set $fwd = "R1.fasta.gz"
27 #set $rev = "R2.fasta.gz" 28 #set $rev = "R2.fasta.gz"
28 #else 29 #else
29 #set $fwd = "R1.fasta" 30 #set $fwd = "R1.fasta"
30 #set $rev = "R2.fasta" 31 #set $rev = "R2.fasta"
31 #end if 32 #end if
32 ln -s $forward $__tool_directory__/process/$fwd; 33 ln -s $forward $__tool_directory__/$fwd;
33 ln -s $reverse $__tool_directory__/process/$rev; 34 ln -s $reverse $__tool_directory__/$rev;
34 #if $reads.reads_select == "single" 35 #if $reads.reads_select == "single"
35 #set $rev = "none" 36 #set $rev = "none"
36 #end if 37 #end if
37 mkdir $__tool_directory__/output; 38 python $__tool_directory__/kmer_read_m3.py
38 python $__tool_directory__/kmer_read_m3.py 39 -w $__tool_directory__
39 -w $__tool_directory__/ 40 -d $__tool_directory__/output
40 -d $__tool_directory__/output 41 -i $__tool_directory__/$fwd $__tool_directory__/$rev
41 -i $__tool_directory__/process/$fwd $__tool_directory__/process/$rev
42
43 ]]></command> 42 ]]></command>
44 <inputs> 43 <inputs>
45 44
46 <conditional name="reads"> 45 <conditional name="reads">
47 <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history"> 46 <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> 47 <option value="single">One FASTQ dataset from your history</option>
49 <option value="paired">Two FASTQ datasets from your history</option> 48 <option value="paired">Two FASTQ datasets from your history</option>
50 </param> 49 </param>
51 <when value="single"> 50 <when value="single">
52 <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/> 51 <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
53 </when> 52 </when>
54 <when value="paired"> 53 <when value="paired">
55 <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" /> 54 <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" /> 55 <param label="Reverse reads" type="data" name="reverse" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
57 </when> 56 </when>
68 <output name="output1" file="mitokmer_result.csv"/> 67 <output name="output1" file="mitokmer_result.csv"/>
69 </test> 68 </test>
70 </tests> 69 </tests>
71 70
72 <help><![CDATA[ 71 <help><![CDATA[
73 72
74 **Usage: mitokmer.py** 73 **Usage: mitokmer.py**
75 74
76 ]]></help> 75 ]]></help>
77 <citations> 76 <citations>
78 <citation type="bibtex"> 77 <citation type="bibtex">
79 meh 78 meh
80 }</citation> 79 }</citation>
81 </citations> 80 </citations>
82 81
83 </tool> 82 </tool>