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1 <tool id="kmer_analysis" name="Kmer">
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2 <description>To calculate the proportion and phasing of each kmer</description>
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3
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3 <requirements>
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4 <requirement type="package">samtools</requirement>
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5 <requirement type="package">numpy</requirement>
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6 <requirement type="package">matplotlib</requirement>
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7 <requirement type="package">pysam</requirement>
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8 </requirements>
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9 <command interpreter="python">
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10 kmer_analysis.py --gff $gff --bam $bamfile --dirout $output.files_path --out $output
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11
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12 </command>
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13
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14 <inputs>
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15 <param name="gff" type="data" label="Reference annotation file (GFF))" format="gff" />
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16 <param name="bamfile" type="data" label="Bam file" format="bam" />
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17 </inputs>
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18
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19 <outputs>
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20 <data format="html" name="output" label="Kmer report on ${on_string}"/>
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21
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22 </outputs>
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23
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24 <help>
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25
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26 Summary
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27 -------
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28 The kmer tool computes the distribution of footprints length from Bam file and determines the proportion of footprints beginning in each frame, for all annotated genes in the `GFF3`_ file.
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29
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30
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31 .. _GFF3: http://gmod.org/wiki/GFF3
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32
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33 Output
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34 -------
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35 This tool provides an html report detailing the proportions and phasing of the kmers.
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36
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37
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38 Dependances
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39 ------------
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40
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41 .. class:: warningmark
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42
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43 This tool depends on Python (>=2.7) and following packages : numpy 1.8.0 and matplotlib 1.3.1. Samtools and pysam are used for bam manipulation.
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44
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45 </help>
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46 </tool> |
