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annotate rnachipintegrator_wrapper.xml @ 4:4b65b5d0d08d draft

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Uploaded version 1.0.3.1 (use conda to resolve dependencies)
author pjbriggs
date Fri, 09 Mar 2018 03:38:31 -0500
parents d37526cd12aa
children
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1 <?xml version="1.0" encoding="utf-8"?>
4
4b65b5d0d08d Uploaded version 1.0.3.1 (use conda to resolve dependencies)
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2 <tool id="rnachipintegrator_wrapper" name="RnaChipIntegrator" version="@VERSION@">
0
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3 <description>Integrated analysis of 'gene' and 'peak' data</description>
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4 <macros>
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5 <import>rnachipintegrator_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command interpreter="bash"><![CDATA[
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10 rnachipintegrator_wrapper.sh
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11 #if $peaks_in.metadata.chromCol
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12 --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}
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13 #end if
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14 #if str( $cutoff ) != ""
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15 --cutoff=$cutoff
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16 #else
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17 --cutoff=0
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18 #end if
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19 #if str( $number ) != ""
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20 --number=$number
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21 #end if
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22 --promoter_region=$promoter_start,$promoter_end
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23 --edge=$edge
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24 $diff_expressed_only
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25 --xlsx_file "$xlsx_out"
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26 --output_files "$peaks_per_feature_out" "$features_per_peak_out"
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27 #if $output.compact_format
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28 --compact
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29 #else
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30 #if $output.summary
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31 --summary_files "$peaks_per_feature_summary" "$features_per_peak_summary"
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32 #end if
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33 ${output.pad_output}
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34 #end if
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35 "$features_in" "$peaks_in"
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36 ]]></command>
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37 <inputs>
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38 <param format="tabular" name="features_in" type="data"
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39 label="Genes/genomic features" />
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40 <param format="tabular" name="peaks_in" type="data"
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41 label="Peaks/regions" />
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42 <expand macro="analysis_options" />
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43 <param name="diff_expressed_only" type="boolean"
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44 truevalue="--only-DE" falsevalue="" checked="false"
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45 label="Only consider genes which are flagged as differentially
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46 expressed"
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47 help="NB input feature data must include differential expression
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48 flags (--only-DE)" />
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49 <expand macro="output_options" />
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50 </inputs>
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51 <outputs>
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52 <!-- Always produce XLSX output -->
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53 <data format="xlsx" name="xlsx_out"
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54 label="All RnaChipIntegrator analyses: ${features_in.name} vs ${peaks_in.name} (Excel spreadsheet)" />
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55 <data format="tabular" name="peaks_per_feature_out"
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56 label="Nearest peaks to each gene: ${features_in.name} vs ${peaks_in.name}" />
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57 <data format="tabular" name="features_per_peak_out"
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58 label="Nearest genes to each peak: ${features_in.name} vs ${peaks_in.name}" />
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59 <data format="tabular" name="peaks_per_feature_summary"
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60 label="Nearest peaks to each gene (summary): ${features_in.name} vs ${peaks_in.name}" >
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61 <filter>output['compact_format'] is False</filter>
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62 <filter>output['summary'] is True</filter>
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63 </data>
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64 <data format="tabular" name="features_per_peak_summary"
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65 label="Nearest gene to each peak (summary): ${features_in.name} vs ${peaks_in.name}" >
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66 <filter>output['compact_format'] is False</filter>
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67 <filter>output['summary'] is True</filter>
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68 </data>
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69 </outputs>
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70 <tests>
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71 <!--
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72 RnaChipIntegrator +name=test +cutoff=130000 +promoter_region=-10000,2500 +xlsx +compact features.txt summits.txt
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73 -->
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74 <test>
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75 <param name="features_in" value="features.txt" ftype="tabular" />
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76 <param name="peaks_in" value="summits.txt" ftype="tabular" />
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77 <param name="cutoff" value="130000" />
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78 <param name="promoter_start" value="-10000" />
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79 <param name="promoter_end" value="2500" />
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80 <output name="xlsx_out" file="summits.xlsx" compare="sim_size" />
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81 <output name="peaks_per_feature_out" ftype="tabular"
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82 file="summits_per_feature.out" />
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83 <output name="features_per_peak_out" ftype="tabular"
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84 file="features_per_summit.out" />
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85 </test>
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86 <!--
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87 RnaChipIntegrator +name=test +cutoff=130000 +promoter_region=-10000,2500 +xlsx +compact features.txt peaks.txt
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88 -->
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89 <test>
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90 <param name="features_in" value="features.txt" ftype="tabular" />
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91 <param name="peaks_in" value="peaks.txt" ftype="tabular" />
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92 <param name="cutoff" value="130000" />
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93 <param name="promoter_start" value="-10000" />
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94 <param name="promoter_end" value="2500" />
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95 <output name="xlsx_out" file="peaks1.xlsx" compare="sim_size" />
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96 <output name="peaks_per_feature_out" ftype="tabular"
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97 file="peaks_per_feature1.out" />
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98 <output name="features_per_peak_out" ftype="tabular"
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99 file="features_per_peak1.out" />
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100 </test>
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101 <!--
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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102 RnaChipIntegrator +name=test +cutoff=130000 +xlsx features.txt peaks.txt
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103 -->
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104 <test>
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105 <param name="features_in" value="features.txt" ftype="tabular" />
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106 <param name="peaks_in" value="peaks.txt" ftype="tabular" />
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107 <param name="cutoff" value="130000" />
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108 <param name="compact_format" value="false" />
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109 <output name="xlsx_out" file="peaks2.xlsx" compare="sim_size" />
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110 <output name="peaks_per_feature_out" ftype="tabular"
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111 file="peaks_per_feature2.out" />
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112 <output name="features_per_peak_out" ftype="tabular"
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113 file="features_per_peak2.out" />
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114 </test>
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115 <!--
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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116 RnaChipIntegrator +name=test +cutoff=130000 +only-DE +xlsx +compact features.txt peaks.txt
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117 -->
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118 <test>
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119 <param name="features_in" value="features.txt" ftype="tabular" />
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120 <param name="peaks_in" value="peaks.txt" ftype="tabular" />
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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121 <param name="cutoff" value="130000" />
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122 <param name="diff_expressed_only" value="true" />
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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123 <output name="xlsx_out" file="peaks3.xlsx" compare="sim_size" />
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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124 <output name="peaks_per_feature_out" ftype="tabular"
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125 file="peaks_per_feature3.out" />
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126 <output name="features_per_peak_out" ftype="tabular"
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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127 file="features_per_peak3.out" />
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128 </test>
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129 <!--
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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130 RnaChipIntegrator +name=test +cutoff=130000 +promoter_region=-10000,2500 +xlsx +summary features.txt peaks.txt
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131 -->
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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132 <test>
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133 <param name="features_in" value="features.txt" ftype="tabular" />
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134 <param name="peaks_in" value="peaks.txt" ftype="tabular" />
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135 <param name="cutoff" value="130000" />
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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136 <param name="compact_format" value="false" />
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137 <param name="summary" value="true" />
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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138 <param name="pad_output" value="true" />
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139 <output name="xlsx_out" file="peaks4.xlsx" compare="sim_size" />
0abe6bac47a6 planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
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140 <output name="peaks_per_feature_out" ftype="tabular"
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141 file="peaks_per_feature4.out" />
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142 <output name="features_per_peak_out" ftype="tabular"
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143 file="features_per_peak4.out" />
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144 <output name="peaks_per_feature_summary" ftype="tabular"
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145 file="peaks_per_feature4.summary" />
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146 <output name="features_per_peak_summary" ftype="tabular"
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147 file="features_per_peak4.summary" />
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148 </test>
2
d37526cd12aa Uploaded version 1.0.2.0.
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149 <!--
d37526cd12aa Uploaded version 1.0.2.0.
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150 RnaChipIntegrator +name=test +cutoff=0 +promoter_region=-10000,2500 +xlsx +summary features.txt peaks.txt
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151 -->
d37526cd12aa Uploaded version 1.0.2.0.
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152 <test>
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153 <param name="features_in" value="features.txt" ftype="tabular" />
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pjbriggs
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154 <param name="peaks_in" value="peaks.txt" ftype="tabular" />
d37526cd12aa Uploaded version 1.0.2.0.
pjbriggs
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155 <param name="cutoff" value="" />
d37526cd12aa Uploaded version 1.0.2.0.
pjbriggs
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156 <param name="compact_format" value="false" />
d37526cd12aa Uploaded version 1.0.2.0.
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157 <param name="summary" value="true" />
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pjbriggs
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158 <param name="pad_output" value="true" />
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159 <output name="xlsx_out" file="peaks6.xlsx" compare="sim_size" />
d37526cd12aa Uploaded version 1.0.2.0.
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160 <output name="peaks_per_feature_out" ftype="tabular"
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161 file="peaks_per_feature6.out" />
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162 <output name="features_per_peak_out" ftype="tabular"
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163 file="features_per_peak6.out" />
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164 <output name="peaks_per_feature_summary" ftype="tabular"
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165 file="peaks_per_feature6.summary" />
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166 <output name="features_per_peak_summary" ftype="tabular"
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167 file="features_per_peak6.summary" />
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168 </test>
0
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169 </tests>
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170 <help>
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171
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172 .. class:: infomark
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173
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174 **What it does**
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175
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176 Performs integrated analyses of genes (or other genomic feature data)
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177 gainst a set of peaks (e.g. ChIP data), identifying the nearest peaks to
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178 each feature and vice versa.
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179
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180 The program was originally written specifically for ChIP-Seq and RNA-Seq
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181 data but works equally well for ChIP-chip and microarray expression data,
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182 and can also be used to integrate any set of genomic features (e.g.
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183 canonical genes, CpG islands) with expression data.
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184
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185 RnaChipIntegrator can be obtained from
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186 https://pypi.python.org/pypi/RnaChipIntegrator/
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187
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188 -------------
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189
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190 .. class:: infomark
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191
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192 **Input**
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193
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194 The gene data must be in a tabular file with the following columns
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195 of data for each gene or genomic feature (one gene per line):
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196
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197 ====== ========== ======================================================================
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198 Column Name Description
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199 ====== ========== ======================================================================
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200 1 ID Name used to identify the gene in the output
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201 2 chr Chromosome name
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202 3 start Start position of the gene
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203 4 end End position of the gene
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204 5 strand Must be either '+' or '-'
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205 6 diff_expr Optional: indicates gene is differentially expressed (1) or not (0)
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206 ====== ========== ======================================================================
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207
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208 The peak data must be in a tabular file with at least 3 columns of data
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209 for each peak (one peak per line):
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210
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211 ====== ========== =================================
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212 Column Name Description
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213 ====== ========== =================================
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214 1 chr Chromosome name
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215 2 start Start position of the peak
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216 3 end End position of the peak
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217 ====== ========== =================================
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218
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219 If peak data is in ``bed`` format then the tool will automatically
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220 assign the correct columns, otherwise the first three columns of data
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221 will be used.
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222
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223 -------------
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224
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225 .. class:: infomark
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226
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227 **Outputs**
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228
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229 The key outputs from the tool are two lists compromising the nearest
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230 peaks for each gene, and the nearest gene for each peak (one dataset
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231 for each list).
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232
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233 There are two formats for reporting: "compact" and "full":
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234
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235 * **Compact output** reports all the hits for each peak or gene on
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236 a single line of output;
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237 * **Full output** reports each peak/gene pair on a separate line
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238 (i.e. a multi-line output format).
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239
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240 In "full" output mode, additional options are available:
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241
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242 * The output files can be "padded" with extra (empty) lines to ensure
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243 that there are always the same number of lines for each peak or
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244 gene, if fewer than the requested number of hits are found.
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245 * "Summary" datasets can also be requested, which include just the
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246 nearest peak reported for each gene (and vice versa).
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247
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248 In either mode these data will also be output in a single MS Excel file,
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249 which contains one sheet per result set.
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250
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251 .. class:: warning
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252
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253 Using "compact" output with the number of hits limited to more than 4
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254 peak/gene pairs (or with no limit at all) can result in a large number
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255 of columns in the output files, which in some versions of Galaxy will
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256 not be properly displayed. However the data files themselves should be
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257 okay.
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258
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259 -------------
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260
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261 .. class:: informark
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262
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263 **More information**
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264
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265 It is recommended that you refer to the ``RnaChipIntegrator``
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266 documentation for information on the contents of each output file:
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267
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268 * http://rnachipintegrator.readthedocs.org/en/latest/
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269
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270 -------------
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271
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272 .. class:: infomark
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273
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274 **Credits**
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275
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276 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
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277 University of Manchester. It runs the RnaChipIntegrator package which has also been
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278 developed by this group, and is documented at
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279 http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
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280
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281 Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.
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282 </help>
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283 <expand macro="citations" />
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284 </tool>