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comparison commet.xml @ 0:0b9a713ece1d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
author iuc
date Fri, 20 Oct 2017 03:11:50 -0400
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children 701b1ab185fe
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-1:000000000000 0:0b9a713ece1d
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool profile="16.04" id="commet" name="Commet" version="24.7.14">
3 <description>COmpare Multiple METagenomes</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="24.7.14">commet</requirement>
9 </requirements>
10 <command><![CDATA[
11 #for $i, $set in enumerate( $sets )
12 echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
13 #end for
14 Commet.py
15 -k ${k}
16 -t ${t}
17 -l ${l}
18 -e ${e}
19 #if str( $options_advanced.options_advanced_selector ) == "advanced"
20 -m ${options_advanced.m}
21 -n ${options_advanced.n}
22 #end if
23 commet_input_sets.txt
24
25 ]]></command>
26
27 <inputs>
28 <!-- Input data files -->
29 <repeat name="sets" title="Read sets" min="1">
30 <param name="reads" type="data" multiple="true" format="fasta, fastq" label="Dataset" help="Accept fasta/fastq"/>
31 </repeat>
32 <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
33 <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
34 <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." />
35 <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." />
36 <conditional name="options_advanced">
37 <param name="options_advanced_selector" type="select" label="Reads filter options" help="By default, all reads are kept with no Ns limitation">
38 <option value="default" selected="true">default</option>
39 <option value="advanced">advanced</option>
40 </param>
41 <when value="default" />
42 <when value="advanced">
43 <param argument="-m" type="integer" value="-1" label="Maximum number of selected reads in sets" help="Maximum number of selected reads in sets. If a set is composed by 3 read files, and this option = 600, then the first 200 reads from each read file will be treated. (-1 = any)" />
44 <param argument="-n" type="integer" value="-1" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept. (-1 = all)" />
45 </when>
46 </conditional>
47 <param name="normalized_outputs" label="Generate normalized files" type="boolean" checked="true"/>
48 <param name="plain_outputs" label="Generate plain files" type="boolean" checked="false"/>
49 <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/>
50 </inputs>
51 <outputs>
52 <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="Matrix plain with ${tool.name} on ${on_string}" >
53 <filter>plain_outputs</filter>
54 </data>
55 <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="Matrix percentage with ${tool.name} on ${on_string}" >
56 <filter>percentage_outputs</filter>
57 </data>
58 <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="Matrix normalized with ${tool.name} on ${on_string}" >
59 <filter>normalized_outputs</filter>
60 </data>
61 <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="Dendrogram ${tool.name} on ${on_string}" />
62 <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="Heatmap normalized with ${tool.name} on ${on_string}" >
63 <filter>normalized_outputs</filter>
64 </data>
65 <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="Heatmap percentage with ${tool.name} on ${on_string}" >
66 <filter>percentage_outputs</filter>
67 </data>
68 <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="Heatmap Plain with ${tool.name} on ${on_string}" >
69 <filter>plain_outputs</filter>
70 </data>
71 </outputs>
72 <tests>
73 <test>
74 <param name="input_type" value="list" />
75 <repeat name="sets">
76 <param name="reads" value="commet/A.fa" ftype="fasta" />
77 </repeat>
78 <repeat name="sets">
79 <param name="reads" value="commet/B.fa,commet/C.fa" ftype="fasta" />
80 </repeat>
81 <repeat name="sets">
82 <param name="reads" value="commet/D.fa" ftype="fasta" />
83 </repeat>
84 <param name="plain_outputs" value="True"/>
85 <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
86 <output name="matrix_plain" file="commet/matrix_plain.csv"/>
87 </test>
88 </tests>
89 <help><![CDATA[
90
91 **Description**
92
93 COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.
94
95 Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results are stored as bit vectors, a compressed representation of read files, that can be used to further combine read subsets by common logical operations. Finally, COMMET computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps.
96
97
98 -------
99
100 **Web site**
101
102 http://colibread.inria.fr/commet/
103
104 ]]></help>
105 <expand macro="citations">
106 <citation type="doi">10.1186/1471-2105-13-S19-S10</citation>
107 </expand>
108 </tool>