Mercurial > repos > iuc > merquryfk_cnplot

annotate cnplot.xml @ 2:cee82fab103d draft default tip

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planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit f02f3754424a68a1463fa75e9523d49e60d68373
author iuc
date Wed, 05 Mar 2025 19:06:52 +0000
parents e93dd04efa15
children
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e93dd04efa15 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 17bf7636eae7b242a4b7507ff2d95fc26759b3f4
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1 <tool id="merquryfk_cnplot" name="MerquryFK CNplot" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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2 <description>Creates copy-number spectrum plots from a genomic read k-mer table and its assembly</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 ln -s $reads input.ktab &&
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9 ln -s $assembly input.fastq &&
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10 ln -s $fastk_ktab_files ktab_files.tar.gz &&
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11 tar -xf ktab_files.tar.gz -C '.' &&
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12 mv ktabfiles/.*.ktab* .input.ktab.1 &&
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13 CNplot
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14 @PLOTS@
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15 @MEASURE@
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16 @GRAPHS@
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17 $pdf
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18 -T\${GALAXY_SLOTS:-1}
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19 input.ktab
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20 input.fastq
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21 output
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22 ]]></command>
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23 <inputs>
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24 <param name="reads" type="data" format="fastk_ktab" label="K-mer table (ktab) obtained from FastK tool"/>
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25 <param name="fastk_ktab_files" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of all intermediate Ktab file from FastK"/>
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26 <param name="assembly" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Assembly of genome" help="Must be same genome as the K-mer table was generated from"/>
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27 <expand macro="plots"/>
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28 <expand macro="sizes"/>
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29 <expand macro="graphs"/>
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30 <expand macro="pdf"/>
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31 </inputs>
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32 <outputs>
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33 <collection name="outputs_png" type="list" label="${tool.name} on ${on_string}: PNG figures">
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34 <filter>pdf is not True</filter>
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35 <discover_datasets pattern="(?P&lt;designation&gt;.*).png" format="png"/>
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36 </collection>
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37 <collection name="outputs_pdf" type="list" label="${tool.name} on ${on_string}: PDF figures">
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38 <filter>pdf is True</filter>
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39 <discover_datasets pattern="(?P&lt;designation&gt;.*).pdf" format="pdf"/>
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40 </collection>
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41 </outputs>
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42 <tests>
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43 <test expect_num_outputs="1">
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44 <param name="reads" value="maternal.ktab"/>
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45 <param name="fastk_ktab_files" ftype="fastk_ktab_tar" value="cnplot_ktab.tar.gz"/>
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46 <param name="assembly" value="maternal.fastq"/>
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47 <param name="width" value="6.0"/>
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48 <param name="height" value="4.5"/>
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49 <param name="graphs" value="-l,-f,-s"/>
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50 <param name="pdf" value="False"/>
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51 <conditional name="measure">
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52 <param name="measurement" value="absolute"/>
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53 <param name="max_x" value="2"/>
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54 <param name="max_y" value="1"/>
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55 </conditional>
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56 <output_collection name="outputs_png" count="3"/>
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57 </test>
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58 <test expect_num_outputs="1">
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59 <param name="reads" value="maternal.ktab"/>
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60 <param name="fastk_ktab_files" ftype="fastk_ktab_tar" value="cnplot_ktab.tar.gz"/>
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61 <param name="assembly" value="maternal.fastq"/>
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62 <param name="width" value="6.0"/>
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63 <param name="height" value="4.5"/>
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64 <param name="graphs" value="-l,-f,-s"/>
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65 <param name="pdf" value="True"/>
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66 <conditional name="measure">
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67 <param name="measurement" value="absolute"/>
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68 <param name="max_x" value="2"/>
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69 <param name="max_y" value="1"/>
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70 </conditional>
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71 <output_collection name="outputs_pdf" count="3"/>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 Given a k-mer table, produced by FastK, for a read data set, and an assembly of the same genome, CNplot produces copy-number spectrum plots for the pair.
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76 ]]></help>
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77 <expand macro="citation"/>
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78 </tool>