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1 <tool id="formatplotfasta" name="Adjust fasta line length and plot content" version="0.0.1" force_history_refresh="True">
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2
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3 <description>Change the number of nucleotides per line in the input fasta and plot nt content </description>
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4
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5 <requirements>
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6 <requirement type="package" version="1.4"> matplotlib </requirement>
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7 </requirements>
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8
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9 <command interpreter="python"> example2.py "${infasta}" $linesize $formatted_fasta $plot </command>
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10
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11 <inputs>
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12 <param name="infasta" format="fasta" type="data" label="input fasta" help="no help"/>
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13 <param name="linesize" type="integer" value="50" label="number of nt per line" help=" be reasonable!"/>
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14 </inputs>
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15
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16 <outputs>
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17 <data name="formatted_fasta" format="fasta" label="${tool.name} on ${on_string}: formatted fasta"/>
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18 <data name="plot" format="pdf" label="${tool.name} on ${on_string}: plot"/>
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19 </outputs>
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20
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21 <tests>
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22 <test>
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23 <param name="infasta" value="mouse_reference_mtDNA.fasta"/>
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24 <param name="linesize" value="200"/>
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25 <output name="formatted_fasta" file="adjusted_200_mouse_reference_mtDNA.fasta"/>
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26 <output name="plot" file="mouse_reference_mtDNA.fasta_nt_counts.pdf"/>
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27 </test>
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28 </tests>
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29
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30 <help>
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31
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32 <![CDATA[
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33 Short description.
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34
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35 -----
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36
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37 .. class:: infomark
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38
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39 **What it does**
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40
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41 Longer description.
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42
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43 -----
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44
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45 .. class:: warningmark
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46
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47 **Note**
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48
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49 Some warining, if needed:
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50
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51 -----
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52
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53 .. class:: infomark
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54
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55 **Formats**
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56
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57 **FASTA multiple alignment**
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58
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59 See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format
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60
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61 -----
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62
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63 **Example**
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64
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65
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66 -----
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67
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68 **Citation**
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69
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70 (boris-at-bx.psu.edu) ]]>
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71
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72 </help>
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73 </tool> |
