annotate chicExportData.xml @ 3:1a31e75e979e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author iuc
date Thu, 05 Dec 2024 18:31:59 +0000
parents 163fd744e235
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1 <tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>exports data of hdf to txt based files</description>
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3 <macros>
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4 <token name="@BINARY@">chicExportData</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10 mkdir exportFolder &&
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11 @BINARY@
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12 --file '$file'
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14 #if $fileType_conditional.fileType_selector == 'interaction':
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15 #if $fileType_conditional.txtBigwig_conditional.txtBigwig_selector == 'txt':
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16 --outputFileType txt
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17 #else:
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18 --outputFileType bigwig
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19 --outputValueBigwig $fileType_conditional.txtBigwig_conditional.column_selector
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20 --chromosomeSizes '$fileType_conditional.txtBigwig_conditional.chromosomeSize'
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21 --range $fileType_conditional.txtBigwig_conditional.rangeUpstream $fileType_conditional.txtBigwig_conditional.rangeDownstream
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22 --backgroundModelFile '$fileType_conditional.txtBigwig_conditional.backgroundModelFile'
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23 #end if
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24 #else if $fileType_conditional.fileType_selector == 'target':
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25 $fileType_conditional.oneTargetFile
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26 #end if
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27 #if $fileType_conditional.fileType_selector != 'interaction':
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28 --outputFileType txt
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29 #end if
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30
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31 --outputMode $outputMode_conditional.outputMode_selector
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32 #if $outputMode_conditional.outputMode_selector == 'geneName':
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33 --outputModeName $outputMode_conditional.outputModeName
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34 #end if
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35 --decimalPlaces $decimalPlaces
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36 --outFileName exportFolder/export.tar.gz
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37 --threads @THREADS@
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38
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39 ]]></command>
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40 <inputs>
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41 <param name="file" type="data" format="h5" label="" />
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42 <conditional name="fileType_conditional">
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43
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44 <param name="fileType_selector" type="select" label="Combination mode for the plots">
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45 <option value="interaction" selected="True">Interaction file (from chicViewpoint)</option>
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46 <option value="aggregate">Aggregated file (from chicAggregateStatistic)</option>
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47 <option value="significant" >Significant file (from chicSignificantInteractions)</option>
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48 <option value="target" >Target file (from chicSignificantInteractions)</option>
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49 <option value="differential" >Differential file (from chicDifferentialTest)</option>
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50 </param>
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51 <when value="interaction" >
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52 <conditional name="txtBigwig_conditional">
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53 <param name="txtBigwig_selector" type="select" label="Output format">
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54 <option value="txt" selected="True">Text</option>
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55 <option value="bigwig">BigWig</option>
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56 </param>
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57 <when value="txt" >
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58 </when>
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59 <when value="bigwig" >
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60 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range"
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61 help="Defines the region upstream of a reference point which should be considered in the analysis." />
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62 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range"
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63 help="Defines the region upstream of a reference point which should be considered in the analysis." />
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64 <param name="column_selector" type="select" label="Datatrack output type">
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65 <option value="relative-interactions" selected="True">relative interactions</option>
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66 <option value="p-value">p-value</option>
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67 <option value="x-fold" >x-fold</option>
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68 <option value="raw" >raw</option>
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69 </param>
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70 <param name="backgroundModelFile" type="data" format="tabular" label="Background model"
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71 help="The background file computed by chicViewpointBackgroundModel" />
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72 <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size"
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73 help="Chromosome size as tabular file. One chromosome per line" />
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74 </when>
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75 </conditional>
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76 </when>
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77 <when value="aggregate" >
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78 </when>
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79 <when value="significant" >
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80 </when>
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81 <when value="target" >
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82 <param name="oneTargetFile" type="boolean" truevalue="--oneTargetFile" falsevalue="" checked="false" label="Create only one target file" />
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83 </when>
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84 <when value="differential" >
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85 </when>
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86 </conditional>
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87
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88 <conditional name="outputMode_conditional">
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89 <param name="outputMode_selector" type="select" label="Output mode">
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90 <option value="all" selected="True">all</option>
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91 <option value="geneName" >gene name</option>
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92 </param>
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93 <when value="all" >
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94 </when>
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95 <when value="geneName" >
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96 <param name="outputModeName" type="text" value="" label="Gene name" help="Based on this gene name the output is extracted." />
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97 </when>
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98 </conditional>
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99 <param name="decimalPlaces" type="integer" value="12" label="Decimal places" help="Number of decimal places for float values." />
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100
23b8d6b8960c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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101 </inputs>
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102 <outputs>
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103 <collection name="oneGeneCollectionBigwig" type="list" label="The exported bigwig files">
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104 <discover_datasets pattern="__name__" format="bigwig" directory="exportFolder" />
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105 </collection>
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106 <collection name="oneGeneCollectionText" type="list" label="The exported text files">
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107 <discover_datasets pattern="__name__" format="txt" directory="exportFolder" />
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108 </collection>
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109 <data name="allTar" from_work_dir="exportFolder/export.tar.gz" format="tar.gz" label="The exported data as tar.gz">
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110 <filter>outputMode_conditional['outputMode_selector'] == 'all'</filter>
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111 </data>
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112 </outputs>
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113 <tests>
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114 <test expect_num_outputs="3">
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115 <param name="file" value="cHi-C/chicAggregateStatistic/aggregate.hdf5" />
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116 <conditional name="fileType_conditional">
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117 <param name="fileType_selector" value="aggregate" />
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118 </conditional>
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119 <conditional name="outputMode_conditional">
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120 <param name="outputMode_selector" value="all" />
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121 </conditional>
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122 <output name="allTar" file="cHi-C/chicExportData/aggregate.tar.gz" ftype="tar.gz" compare="sim_size" />
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123 </test>
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124
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125 <test expect_num_outputs="2">
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126 <param name="file" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
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127 <conditional name="fileType_conditional">
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128 <param name="fileType_selector" value="interaction" />
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129
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130 <conditional name="txtBigwig_conditional">
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131 <param name="txtBigwig_selector" value="bigwig" />
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132 <param name="backgroundModelFile" value="cHi-C/background.txt" />
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133 <param name="chromosomeSize" value="cHi-C/hg19.chrom.sizes" />
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134 </conditional>
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135 </conditional>
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136 <conditional name="outputMode_conditional">
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137 <param name="outputMode_selector" value="geneName" />
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138 <param name="outputModeName" value="Eya1" />
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139 </conditional>
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140 <output_collection name="oneGeneCollectionBigwig" type="list" count="4">
1
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141 <element name="FL-E13-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
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142 <element name="MB-E10-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
0
23b8d6b8960c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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143 <element name="background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
23b8d6b8960c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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144 <element name="background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
23b8d6b8960c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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145 </output_collection>
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146 </test>
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147 <test expect_num_outputs="2">
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148 <param name="file" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
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149 <conditional name="fileType_conditional">
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150 <param name="fileType_selector" value="interaction" />
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151 <conditional name="txtBigwig_conditional">
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152 <param name="txtBigwig_selector" value="txt" />
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153 </conditional>
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154 </conditional>
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155 <conditional name="outputMode_conditional">
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156 <param name="outputMode_selector" value="geneName" />
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157 <param name="outputModeName" value="Eya1" />
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158 </conditional>
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159 <output_collection name="oneGeneCollectionText" type="list" count="2">
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160 <element name="FL-E13-5_chr1_genes_Eya1_interactions.txt" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt" ftype="txt" compare="sim_size" />
23b8d6b8960c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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161 <element name="MB-E10-5_chr1_genes_Eya1_interactions.txt" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt" ftype="txt" compare="sim_size" />
23b8d6b8960c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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162 </output_collection>
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163 </test>
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164 </tests>
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165 <help><![CDATA[
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166
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167 Exporting the binary data to text files
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168 =======================================
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170 chicExportData extracts the data stored in hdf5 files of the capture Hi-C modules to text files.
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172 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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174 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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175 ]]> </help>
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176 <expand macro="citations" />
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177 </tool>