Mercurial > repos > iuc > jcvi_gff_stats
comparison jcvi_gff_stats.xml @ 0:2defe48e4c7a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
author | iuc |
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date | Thu, 02 Aug 2018 09:57:30 -0400 |
parents | |
children | 8cffbd184762 |
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-1:000000000000 | 0:2defe48e4c7a |
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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> |