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comparison format_cd_hit_output.xml @ 1:4ba41bcee051 draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
author bebatut
date Tue, 26 Apr 2016 08:54:26 -0400
parents bbd903996900
children
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0:bbd903996900 1:4ba41bcee051
1 <tool id="format_cd_hit_output" name="Format cd-hit outputs" version="0.1.0"> 1 <tool id="format_cd_hit_output" name="Format cd-hit outputs" version="1.0.0">
2 <description>to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file</description>
3
2 <requirements> 4 <requirements>
3 </requirements> 5 </requirements>
4 6
5 <stdio> 7 <stdio>
6 <exit_code range="1:" /> 8 <exit_code range="1:" />
7 </stdio> 9 </stdio>
8 10
9 <version_command><![CDATA[python -version]]></version_command> 11 <version_command>
12 </version_command>
10 13
11 <command><![CDATA[ 14 <command><![CDATA[
12 python $__tool_directory__/format_cd_hit_output.py 15 python $__tool_directory__/format_cd_hit_output.py
13 --input_cluster_info $input_cluster_info 16 --input_cluster_info $input_cluster_info
14 17
15 #if $rename_representative_sequences.test 18 #if $rename_repr_seq.rename_repr_seq_test == "true"
16 --input_representative_sequences $rename_representative_sequences.input_representative_sequences 19 --input_representative_sequences $rename_repr_seq.input_representative_sequences
17 --output_representative_sequences $output_representative_sequences 20 --output_representative_sequences $output_representative_sequences
18 #end if 21 #end if
19 22
20 #if $extract_category_distribution.test 23 #if $extract_cat_distri.extract_cat_distri_test == "true"
21 --input_mapping $extract_category_distribution.input_mapping 24 --input_mapping $extract_cat_distri.input_mapping
22 --output_category_distribution $output_category_distribution 25 --output_category_distribution $output_category_distribution
23 --number_sum $extract_category_distribution.number_sum 26 $extract_cat_distri.number_sum
24 #end if 27 #end if
25 ]]> 28 ]]>
26 </command> 29 </command>
27 30
28 <inputs> 31 <inputs>
29 <param type="data" format="txt" name="input_cluster_info" label="Cluster 32 <param type="data" format="txt" name="input_cluster_info" label="Cluster info" help="(--input_cluster_info)"/>
30 info"/> 33 <conditional name="rename_repr_seq">
31 34 <param name='rename_repr_seq_test' type="select" label="Rename representative sequences with the corresponding cluster name?" help="">
32 <conditional name="rename_representative_sequences"> 35 <option value="true" selected="true">Yes</option>
33 <param name='test' type='boolean' checked="true" 36 <option value="false">No</option>
34 label="Rename representative sequences with the 37 </param>
35 corresponding cluster name?" help=""/>
36 <when value="true"> 38 <when value="true">
37 <param type="data" format="fasta" 39 <param type="data" format="fasta"
38 name="input_representative_sequences" 40 name="input_representative_sequences"
39 label="Representative sequences"/> 41 label="Representative sequences" help="--input_representative_sequences)"/>
40 </when> 42 </when>
41 <when value="false" /> 43 <when value="false" />
42 </conditional> 44 </conditional>
43 45
44 <conditional name="extract_category_distribution"> 46 <conditional name="extract_cat_distri">
45 <param name='test' type='boolean' checked="true" 47 <param name='extract_cat_distri_test' type="select" label="Extract category distribution of each cluster?" help="">
46 label="Extract category distribution of each 48 <option value="true" selected="true">Yes</option>
47 cluster?" help=""/> 49 <option value="false">No</option>
50 </param>
48 <when value="true"> 51 <when value="true">
49 <param type="data" format="tabular" name="input_mapping" 52 <param type="data" format="tabular,tsv,csv" name="input_mapping" label="Mapping file" help="The mapping file is a tabular file with 2 columns. First column contains the sequence names and the second one the corresponding category (--input_mapping)"/>
50 label="Mapping file" help="The mapping file is a tabular 53 <param name='number_sum' type='boolean' checked="true" truevalue="--number_sum 1" falsevalue="" label="Sum sequence number for each category?" help="The alternative is the sum of size for sequences in each category (if the size information is available in sequence name, --number_sum)"/>
51 file with 2 columns. First column contains the sequence
52 names and the second one the corresponding category"/>
53 <param name='number_sum' type='boolean' checked="true"
54 label="Sum sequence number
55 for each category?" help="The alternative is the sum of size
56 for sequences in each category (if the size information is
57 available in sequence name)"/>
58 </when> 54 </when>
59 <when value="false" /> 55 <when value="false" />
60 </conditional> 56 </conditional>
61 </inputs> 57 </inputs>
62 58
63 <outputs> 59 <outputs>
64 <data name="output_representative_sequences" format="fasta" 60 <data name="output_representative_sequences" format="fasta"
65 label="${tool.name} on ${on_string}: Renamed representative sequences"> 61 label="${tool.name} on ${on_string}: Renamed representative sequences">
66 <filter>((rename_representative_sequences['test']))</filter> 62 <filter>((rename_repr_seq['rename_repr_seq_test'] == "true"))</filter>
67 </data> 63 </data>
68 <data name="output_category_distribution" format="tabular" 64 <data name="output_category_distribution" format="tabular"
69 label="${tool.name} on ${on_string}: Category distribution"> 65 label="${tool.name} on ${on_string}: Category distribution">
70 <filter>((extract_category_distribution['test']))</filter> 66 <filter>((extract_cat_distri['extract_cat_distri_test'] == "true"))</filter>
71 </data> 67 </data>
72 </outputs> 68 </outputs>
73 69
74 <tests> 70 <tests>
75 <test> 71 <test>
76 <param name="input_representative_sequences"
77 value="input_representative_sequences.fasta"/>
78 <param name="rename_representative_sequences.test" value="yes"/>
79 <param name="input_cluster_info" value="input_cluster_info.txt"/> 72 <param name="input_cluster_info" value="input_cluster_info.txt"/>
80 <param name="extract_category_distribution.test" value="yes"/> 73 <param name="rename_repr_seq_test" value="true"/>
81 <param name="input_mapping_file" value="input_mapping.txt"/> 74 <param name="input_representative_sequences" value="input_representative_sequences.fasta"/>
82 <output name="output_representative_sequences" 75 <param name="extract_cat_distri_test" value="true"/>
83 file="output_representative_sequences.fasta"/> 76 <param name="input_mapping" value="input_mapping.txt"/>
84 <output name="output_category_distribution" 77 <param name="number_sum" value="true"/>
85 file="output_category_distribution.txt"/> 78 <output name="output_representative_sequences" file="rename_representative_sequences_output.fasta"/>
79 <output name="output_category_distribution" file="extract_category_distribution_output.tabular"/>
86 </test> 80 </test>
87 </tests> 81 </tests>
88 82
89 <help><![CDATA[ 83 <help><![CDATA[
90 84
91 **What it does** 85 **What it does**
92 86
93 This tool format cd-hit outputs (cluster information and cluster representative 87 This tool format cd-hit outputs (cluster information and cluster representative sequences) to rename representative sequences with cluster name and/or extract category distribution inside clusters given a mapping file.
94 sequences) to rename the representative sequences with cluster name and/or extract
95 category distribution of each cluster
96
97 -----
98
99 **Inputs**
100 88
101 The tool takes as input: 89 The tool takes as input:
102 90
103 - The cd-hit output file with cluster information 91 - The cd-hit output file with cluster information
104 - The cd-hit output file with representative sequences for each cluster (optional) 92 - The cd-hit output file with representative sequences for each cluster (optional)
105 - A mapping file in tabular format with first column being the sequence names 93 - A mapping file in tabular format with first column being the sequence names (corresponding to the ones in cluster information file) and the second column being the corresponding categories (optional)
106 (corresponding to the ones in cluster information file) and the second column being
107 the corresponding categories (optional)
108 94
109 ----- 95 The tool generates different outputs given chosen parameters:
110
111 **Outputs**
112
113 The tool generates different outputs given the choosen parameters:
114 96
115 - A file with representative sequences of each cluster named with the cluster name 97 - A file with representative sequences of each cluster named with the cluster name
116 - A tabular file with lines corresponding to clusters, columns to categories (and 98 - A tabular file with lines corresponding to clusters, columns to categories (and one column with sequence number in the cluster), and cases to number of sequences of the given category in the cluster
117 one column with sequence number in the cluster), and cases to number of sequences
118 of the given category in the cluster
119 99
120 ]]> 100 ]]>
121 </help> 101 </help>
122 102
123 <citations></citations> 103 <citations></citations>