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comparison jcvi_gff_stats.xml @ 0:2defe48e4c7a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
author iuc
date Thu, 02 Aug 2018 09:57:30 -0400
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children 8cffbd184762
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-1:000000000000 0:2defe48e4c7a
1 <?xml version="1.0"?>
2 <tool id="jcvi_gff_stats" name="Genome annotation statistics" profile="16.04" version="@VERSION@">
3 <description></description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command><![CDATA[
9
10 ln -s '${gff}' 'input.gff'
11
12 &&
13
14 python -m jcvi.annotation.stats genestats 'input.gff' > '${summary}'
15
16 &&
17
18 #if str($ref_genome.genome_type_select) == "indexed":
19 python -m jcvi.annotation.stats summary 'input.gff' '${ref_genome.genome.fields.path}' 2>&1 | tail -n +3 >> '${summary}'
20 #else
21 python -m jcvi.annotation.stats summary 'input.gff' '${ref_genome.genome}' 2>&1 | tail -n +3 >> '${summary}'
22 #end if
23
24 &&
25
26 python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '${summary}'
27
28 &&
29
30 python -m jcvi.annotation.stats histogram 'input.gff'
31
32 &&
33
34 pdfunite *.input.pdf '${graphs}'
35 ]]></command>
36 <inputs>
37 <param name="gff" type="data" format="gff" label="Annotation to analyse"/>
38 <conditional name="ref_genome">
39 <param label="Reference genome" name="genome_type_select" type="select">
40 <option selected="True" value="indexed">Use a built-in genome</option>
41 <option value="history">Use a genome from history</option>
42 </param>
43 <when value="indexed">
44 <param
45 help="If your genome of interest is not listed, contact the Galaxy server administrators"
46 label="Select a reference genome"
47 name="genome"
48 type="select"
49 >
50 <options from_data_table="all_fasta">
51 <filter column="2" type="sort_by" />
52 <validator message="No genomes are available" type="no_options" />
53 </options>
54 </param>
55 </when>
56 <when value="history">
57 <param name="genome" type="data" format="fasta" label="Corresponding genome sequence"/>
58 </when>
59 </conditional>
60 </inputs>
61 <outputs>
62 <data format="txt" name="summary" label="${tool.name} on ${on_string}: summary"/>
63 <data format="pdf" name="graphs" label="${tool.name} on ${on_string}: gene length"/>
64 </outputs>
65 <tests>
66 <test>
67 <param name="gff" value="annot.gff3"/>
68 <conditional name="ref_genome">
69 <param name="genome_type_select" value="history"/>
70 <param name="genome" value="genome.fasta"/>
71 </conditional>
72 <output name="summary" file="summary.txt"/>
73 <output name="graphs" file="all.pdf" compare="sim_size"/>
74 </test>
75 <test>
76 <param name="gff" value="annot.gff3"/>
77 <conditional name="ref_genome">
78 <param name="genome_type_select" value="indexed"/>
79 <param name="genome" value="merlin"/>
80 </conditional>
81 <output name="summary" file="summary.txt"/>
82 <output name="graphs" file="all.pdf" compare="sim_size"/>
83 </test>
84 </tests>
85 <help><![CDATA[
86 Based on JCVI Python utility libraries on genome assembly, annotation and comparative genomics.
87
88 .. _JCVI Python utilities: https://github.com/tanghaibao/jcvi
89 ]]></help>
90 <expand macro="citations"/>
91 </tool>