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annotate mitokmer.1.xml @ 3:c9d98f5bc240 draft

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author cstrittmatter
date Sun, 28 Apr 2019 00:42:24 -0400
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1 <tool id="mitokmer_v1" name="mitokmer 1" version="1.0">
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2 <description>Eukaryotic abundance prediction by mitochondrial content</description>
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3 <requirements>
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4 <requirement type="package" version="2.7">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7
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8 rm $__tool_directory__/R*.fastq;
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9 #if $reads.reads_select == "paired"
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10 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
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11 #set $forward = $reads.forward
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12 #set $reverse = $reads.reverse
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13 #else
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14 #set $name = $reads.allreads.name.split('.')[0].replace(' ','_')
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15 #set $forward = $reads.allreads
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16 #set $reverse = $reads.allreads
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17 #end if
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18 echo $name;
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19 echo "-=-=-";
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20 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
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21 #set $fwd = "R1.fastq.gz"
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22 #set $rev = "R2.fastq.gz"
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23 #else if $forward.is_of_type('fastq', 'fastqsanger')
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24 #set $fwd = "R1.fastq"
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25 #set $rev = "R2.fastq"
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26 #else if $forward.is_of_type('fasta.gz')
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27 #set $fwd = "R1.fasta.gz"
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28 #set $rev = "R2.fasta.gz"
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29 #else
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30 #set $fwd = "R1.fasta"
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31 #set $rev = "R2.fasta"
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32 #end if
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33 ln -s $forward $__tool_directory__/$fwd;
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34 ln -s $reverse $__tool_directory__/$rev;
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35 #if $reads.reads_select == "single"
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36 #set $rev = "none"
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37 #end if
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38 python $__tool_directory__/kmer_read_m3.py
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39 -w $__tool_directory__
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40 -d $__tool_directory__/output
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41 -i $__tool_directory__/$fwd $__tool_directory__/$rev
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42 ]]></command>
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43 <inputs>
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44
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45 <conditional name="reads">
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46 <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">
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47 <option value="single">One FASTQ dataset from your history</option>
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48 <option value="paired">Two FASTQ datasets from your history</option>
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49 </param>
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50 <when value="single">
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51 <param label="all reads" type="data" name="allreads" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz"/>
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52 </when>
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53 <when value="paired">
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54 <param label="Forward reads" type="data" name="forward" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
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55 <param label="Reverse reads" type="data" name="reverse" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
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56 </when>
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57 </conditional>
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58
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59 </inputs>
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60 <outputs>
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61 <data format="tabular" label="mitokmer Results" name="results" from_work_dir="output/mitokmer_result.csv"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="reads_select" value="single" />
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66 <param name="allreads" value="1a.fasta" format="fasta"/>
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67 <output name="output1" file="mitokmer_result.csv"/>
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68 </test>
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69 </tests>
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70
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71 <help><![CDATA[
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72
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73 **Usage: mitokmer.py**
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74
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75 ]]></help>
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76 <citations>
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77 <citation type="bibtex">
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78 meh
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79 }</citation>
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80 </citations>
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81
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82 </tool>