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comparison assembly-stats.xml @ 0:9e4955725212 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats commit 28119c39c4b59a67f629c8ca569d58f4d2949c9c
author iuc
date Wed, 21 Jun 2023 09:26:46 +0000
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-1:000000000000 0:9e4955725212
1 <?xml version="1.0"?>
2 <tool id="assembly_stats" name="Assembly stats" version="@TOOL_VERSION@+galaxy0" profile="21.05">
3 <description>visualisations</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rjchallis-assembly-stats</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 #if $output_format == "html"
12 SRC="\$(dirname \$(which asm2stats.pl))/../opt/assembly-stats" &&
13 mkdir -p $output.files_path &&
14
15 cp -r "\$SRC/css/" '$output.files_path' &&
16 cp -r "\$SRC/js/" '$output.files_path' &&
17 cp '$__tool_directory__/d3-tip.js' '${output.files_path}/js/d3-tip.js' &&
18 mkdir -p '$output.files_path/json/' &&
19 cp '$__tool_directory__/assembly-stats.html' '$output' &&
20 cp '$__tool_directory__/assembly-stats.html' '${output.files_path}' &&
21
22 asm2stats.minmaxgc.pl '${input_fasta}' > '${output.files_path}/json/output.assembly-stats.json' ######
23 #else
24 asm2stats.minmaxgc.pl '${input_fasta}' > '${output}'
25 #end if
26
27 ]]></command>
28
29 <inputs>
30 <param name="input_fasta" type="data" format="fasta" label="Genome assembly"/>
31 <param name="output_format" type="select" label="Output format" >
32 <option value="html" selected="true">HTML</option>
33 <option value="json">JSON</option>
34 </param>
35 </inputs>
36
37 <outputs>
38 <data name="output" format="html" label="Assembly-stats on ${on_string}" >
39 <change_format>
40 <when input="output_format" value="json" format="json" />
41 </change_format>
42 </data>
43 </outputs>
44
45 <tests>
46 <test expect_num_outputs="1">
47 <param name="input_fasta" value="sequence.fasta"/>
48 <param name="output_format" value="json"/>
49 <output name="output" ftype="json">
50 <assert_contents>
51 <has_text text='"contig_count" : 1' />
52 <has_text text='"scaffold_count" : 1' />
53 <has_text text='154478' />
54 <has_text text='"GC" : 36.29' />
55 </assert_contents>
56 </output>
57 </test>
58 <test expect_num_outputs="1">
59 <param name="input_fasta" value="sequence.fasta"/>
60 <param name="output_format" value="html"/>
61 <output name="output" value="assembly-stats.html" ftype="html">
62 <assert_contents>
63 <has_size value="7819"/>
64 </assert_contents>
65 </output>
66 </test>
67 </tests>
68
69 <help><![CDATA[
70 assembly_stats_ Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.
71
72 .. _assembly_stats: https://github.com/rjchallis/assembly-stats
73 ]]></help>
74 <expand macro="citation"/>
75 </tool>