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comparison mitokmer.xml @ 3:c9d98f5bc240 draft

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planemo upload commit 003cdb83fd17248ef57959332d58a3c96311332a-dirty
author cstrittmatter
date Sun, 28 Apr 2019 00:42:24 -0400
parents a0852bb4b09b
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2:a0852bb4b09b 3:c9d98f5bc240
36 #set $rev = "none" 36 #set $rev = "none"
37 #end if 37 #end if
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 $__tool_directory__/$fwd $__tool_directory__/$rev;
42 echo "run cat";
43 rm $__tool_directory__/results*;
44 cat $__tool_directory__/output/mitokmer_result.csv > $__tool_directory__/results.csv;
42 ]]></command> 45 ]]></command>
43 <inputs> 46 <inputs>
44 47
45 <conditional name="reads"> 48 <conditional name="reads">
46 <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history"> 49 <param name="reads_select" type="select" label="One FASTQ dataset from your history, or two datasets from your history">
56 </when> 59 </when>
57 </conditional> 60 </conditional>
58 61
59 </inputs> 62 </inputs>
60 <outputs> 63 <outputs>
61 <data format="tabular" label="mitokmer Results" name="results" from_work_dir="output/mitokmer_result.csv"/> 64 <data format="tabular" label="mitokmer Results" name="results" from_work_dir="results.csv"/>
62 </outputs> 65 </outputs>
63 <tests> 66 <tests>
64 <test> 67 <test>
65 <param name="reads_select" value="single" /> 68 <param name="reads_select" value="single" />
66 <param name="allreads" value="1a.fasta" format="fasta"/> 69 <param name="allreads" value="1a.fasta" format="fasta"/>
67 <output name="output1" file="mitokmer_result.csv"/> 70 <output name="output1" file="output/mitokmer_result.csv"/>
68 </test> 71 </test>
69 </tests> 72 </tests>
70 73
71 <help><![CDATA[ 74 <help><![CDATA[
72 75