Mercurial > repos > iuc > merquryfk_cnplot

comparison cnplot.xml @ 0:e93dd04efa15 draft

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