Mercurial > repos > bebatut > format_cd_hit_output

annotate format_cd_hit_output.xml @ 0:bbd903996900 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
author bebatut
date Wed, 27 Jan 2016 03:28:42 -0500
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children 4ba41bcee051
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bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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1 <tool id="format_cd_hit_output" name="Format cd-hit outputs" version="0.1.0">
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2 <requirements>
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3 </requirements>
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4
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8
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9 <version_command><![CDATA[python -version]]></version_command>
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10
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11 <command><![CDATA[
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12 python $__tool_directory__/format_cd_hit_output.py
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13 --input_cluster_info $input_cluster_info
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14
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15 #if $rename_representative_sequences.test
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16 --input_representative_sequences $rename_representative_sequences.input_representative_sequences
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17 --output_representative_sequences $output_representative_sequences
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18 #end if
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19
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20 #if $extract_category_distribution.test
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21 --input_mapping $extract_category_distribution.input_mapping
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22 --output_category_distribution $output_category_distribution
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23 --number_sum $extract_category_distribution.number_sum
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24 #end if
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25 ]]>
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26 </command>
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27
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28 <inputs>
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29 <param type="data" format="txt" name="input_cluster_info" label="Cluster
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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30 info"/>
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31
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32 <conditional name="rename_representative_sequences">
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33 <param name='test' type='boolean' checked="true"
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34 label="Rename representative sequences with the
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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35 corresponding cluster name?" help=""/>
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36 <when value="true">
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37 <param type="data" format="fasta"
bbd903996900 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit ffb68b2ddd94854a34a2533105f7bc08884c6e38-dirty
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38 name="input_representative_sequences"
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39 label="Representative sequences"/>
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40 </when>
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41 <when value="false" />
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42 </conditional>
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43
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44 <conditional name="extract_category_distribution">
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45 <param name='test' type='boolean' checked="true"
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46 label="Extract category distribution of each
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47 cluster?" help=""/>
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48 <when value="true">
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49 <param type="data" format="tabular" name="input_mapping"
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50 label="Mapping file" help="The mapping file is a tabular
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51 file with 2 columns. First column contains the sequence
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52 names and the second one the corresponding category"/>
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53 <param name='number_sum' type='boolean' checked="true"
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54 label="Sum sequence number
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55 for each category?" help="The alternative is the sum of size
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56 for sequences in each category (if the size information is
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57 available in sequence name)"/>
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58 </when>
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59 <when value="false" />
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60 </conditional>
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61 </inputs>
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62
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63 <outputs>
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64 <data name="output_representative_sequences" format="fasta"
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65 label="${tool.name} on ${on_string}: Renamed representative sequences">
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66 <filter>((rename_representative_sequences['test']))</filter>
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67 </data>
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68 <data name="output_category_distribution" format="tabular"
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69 label="${tool.name} on ${on_string}: Category distribution">
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70 <filter>((extract_category_distribution['test']))</filter>
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71 </data>
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72 </outputs>
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73
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74 <tests>
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75 <test>
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76 <param name="input_representative_sequences"
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77 value="input_representative_sequences.fasta"/>
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78 <param name="rename_representative_sequences.test" value="yes"/>
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79 <param name="input_cluster_info" value="input_cluster_info.txt"/>
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80 <param name="extract_category_distribution.test" value="yes"/>
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81 <param name="input_mapping_file" value="input_mapping.txt"/>
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82 <output name="output_representative_sequences"
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83 file="output_representative_sequences.fasta"/>
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84 <output name="output_category_distribution"
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85 file="output_category_distribution.txt"/>
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86 </test>
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87 </tests>
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88
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89 <help><![CDATA[
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90
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91 **What it does**
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92
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93 This tool format cd-hit outputs (cluster information and cluster representative
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94 sequences) to rename the representative sequences with cluster name and/or extract
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95 category distribution of each cluster
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96
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97 -----
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98
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99 **Inputs**
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100
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101 The tool takes as input:
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102
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103 - The cd-hit output file with cluster information
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104 - The cd-hit output file with representative sequences for each cluster (optional)
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105 - A mapping file in tabular format with first column being the sequence names
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106 (corresponding to the ones in cluster information file) and the second column being
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107 the corresponding categories (optional)
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108
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109 -----
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110
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111 **Outputs**
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112
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113 The tool generates different outputs given the choosen parameters:
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114
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115 - A file with representative sequences of each cluster named with the cluster name
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116 - A tabular file with lines corresponding to clusters, columns to categories (and
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117 one column with sequence number in the cluster), and cases to number of sequences
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118 of the given category in the cluster
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119
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120 ]]>
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121 </help>
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122
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123 <citations></citations>
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124 </tool>