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annotate rnachipintegrator_canonical_genes.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 0abe6bac47a6
children
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4
4b65b5d0d08d Uploaded version 1.0.3.1 (use conda to resolve dependencies)
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1 <tool id="rnachipintegrator_canonical_genes" name="Analyse canonical genes against 'peak' data" version="@VERSION@">
0
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2 <description>using RnaChipIntegrator</description>
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3 <macros>
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4 <import>rnachipintegrator_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command interpreter="bash"><![CDATA[
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9 rnachipintegrator_wrapper.sh
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10 #if $peaks_in.metadata.chromCol
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11 --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}
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12 #end if
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13 #if str( $cutoff ) != ""
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14 --cutoff=$cutoff
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15 #else
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16 --cutoff=0
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17 #end if
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18 #if str( $number ) != ""
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19 --number=$number
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20 #end if
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21 --promoter_region=$promoter_start,$promoter_end
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22 --edge=$edge
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23 --xlsx_file "$xlsx_out"
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24 --output_files "$peaks_per_feature_out" "$features_per_peak_out"
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25 #if $output.compact_format
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26 --compact
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27 #else
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28 #if $output.summary
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29 --summary_files "$peaks_per_feature_summary" "$features_per_peak_summary"
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30 #end if
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31 ${output.pad_output}
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32 #end if
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33 "${canonical_genes.fields.path}" "$peaks_in"
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34 ]]></command>
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35 <inputs>
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36 <param format="tabular" name="peaks_in" type="data" label="Peaks" />
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37 <param name="canonical_genes" type="select" label="Canonical genes to analyse peaks against">
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38 <options from_data_table="rnachipintegrator_canonical_genes">
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39 </options>
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40 </param>
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41 <expand macro="analysis_options" />
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42 <expand macro="output_options" />
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43 </inputs>
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44 <outputs>
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45 <!-- Always produce XLS output -->
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46 <data format="xlsx" name="xlsx_out"
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47 label="All RnaChipIntegrator analyses: ${canonical_genes.fields.name} vs ${peaks_in.name} (Excel spreadsheet)" />
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48 <data format="tabular" name="peaks_per_feature_out"
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49 label="Nearest peaks to each gene: ${canonical_genes.fields.name} vs ${peaks_in.name}" />
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50 <data format="tabular" name="features_per_peak_out"
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51 label="Nearest genes to each peak: ${canonical_genes.fields.name} vs ${peaks_in.name}" />
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52 <data format="tabular" name="peaks_per_feature_summary"
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53 label="Nearest peaks to each gene (summary): ${canonical_genes.fields.name} vs ${peaks_in.name}" >
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54 <filter>output['compact_format'] is False</filter>
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55 <filter>output['summary'] is True</filter>
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56 </data>
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57 <data format="tabular" name="features_per_peak_summary"
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58 label="Nearest genes to each peak (summary): ${canonical_genes.fields.name} vs ${peaks_in.name}" >
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59 <filter>output['compact_format'] is False</filter>
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60 <filter>output['summary'] is True</filter>
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61 </data>
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62 </outputs>
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63 <tests>
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64 <!--
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65 RnaChipIntegrator +name=mm9 +cutoff=50000 +xlsx +summary mm9_canonical_genes.tsv mm9_summits.txt
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66 -->
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67 <test>
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68 <param name="peaks_in" value="mm9_summits.txt" ftype="tabular" />
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69 <param name="canonical_genes" value="mm9_test" />
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70 <param name="cutoff" value="50000" />
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71 <output name="xlsx_out" file="mm9_summits.xlsx" compare="sim_size" />
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72 <output name="peaks_per_feature_out" ftype="tabular"
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73 file="mm9_summits_per_feature.out" />
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74 <output name="features_per_peak_out" ftype="tabular"
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75 file="mm9_features_per_summit.out" />
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76 </test>
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77 <!--
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78 RnaChipIntegrator +name=mm9 +cutoff=50000 +xlsx +compact mm9_canonical_genes.tsv mm9_peaks.txt
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79 -->
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80 <test>
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81 <param name="peaks_in" value="mm9_peaks.txt" ftype="tabular" />
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82 <param name="canonical_genes" value="mm9_test" />
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83 <param name="cutoff" value="50000" />
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84 <output name="xlsx_out" file="mm9_peaks1.xlsx" compare="sim_size" />
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85 <output name="peaks_per_feature_out" ftype="tabular"
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86 file="mm9_peaks_per_feature1.out" />
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87 <output name="features_per_peak_out" ftype="tabular"
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88 file="mm9_features_per_peak1.out" />
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89 </test>
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90 <!--
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91 RnaChipIntegrator +name=mm9 +cutoff=50000 +xlsx +summary +pad mm9_canonical_genes.tsv mm9_peaks.txt
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92 -->
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93 <test>
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94 <param name="peaks_in" value="mm9_peaks.txt" ftype="tabular" />
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95 <param name="canonical_genes" value="mm9_test" />
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96 <param name="cutoff" value="50000" />
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97 <param name="compact_format" value="false" />
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98 <param name="summary" value="true" />
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99 <param name="pad_output" value="true" />
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100 <output name="xlsx_out" file="mm9_peaks3.xlsx" compare="sim_size" />
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101 <output name="peaks_per_feature_out" ftype="tabular"
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102 file="mm9_peaks_per_feature3.out" />
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103 <output name="features_per_peak_out" ftype="tabular"
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104 file="mm9_features_per_peak3.out" />
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105 <output name="peaks_per_feature_summary" ftype="tabular"
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106 file="mm9_peaks_per_feature3.summary" />
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107 <output name="features_per_peak_summary" ftype="tabular"
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108 file="mm9_features_per_peak3.summary" />
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109 </test>
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110 </tests>
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111 <help>
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112
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113 .. class:: infomark
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114
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115 **What it does**
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116
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117 Performs integrated analyses of a set of peaks (e.g. ChIP data) against a
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118 list of "canonical genes" for a specific organism and genome build,
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119 identifying the nearest peaks to each canonical gene (and vice versa).
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120
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121 RnaChipIntegrator can be obtained from
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122 http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
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123
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124 -------------
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125
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126 .. class:: infomark
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127
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128 **Input**
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129
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130 The peak data must be in a tabular file with at least 3 columns of data
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131 for each peak (one peak per line):
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132
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133 ====== ========== =================================
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134 Column Name Description
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135 ====== ========== =================================
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136 1 chr Chromosome name
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137 2 start Start position of the peak
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138 3 end End position of the peak
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139 ====== ========== =================================
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140
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141 -------------
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142
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143 .. class:: infomark
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144
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145 **Outputs**
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146
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147 The key outputs from the tool are two lists compromising the nearest
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148 peaks for each gene, and the nearest gene for each peak (one
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149 dataset for each list).
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150
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151 There are two formats for reporting: "compact" and "full":
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152
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153 * **Compact output** reports all the hits for each peak or gene on
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154 a single line of output;
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155 * **Full output** reports each peak/gene pair on a separate line
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156 (i.e. a multi-line output format).
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157
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158 In "full" output mode, additional options are available:
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159
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160 * The output files can be "padded" with extra (empty) lines to ensure
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161 that there are always the same number of lines for each peak or
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162 gene, if fewer than the requested number of hits are found.
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163 * "Summary" datasets can also be requested, which include just the
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164 nearest peak reported for each gene (and vice versa).
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165
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166 In either mode these data will also be output in a single MS Excel file,
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167 which contains one sheet per result set.
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168
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169 .. class:: warning
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170
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171 Using "compact" output with the number of hits limited to more than 4
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172 peak/gene pairs (or with no limit at all) can result in a large number
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173 of columns in the output files, which in some versions of Galaxy will
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174 not be properly displayed. However the data files themselves should be
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175 okay.
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176
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177 -------------
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178
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179 .. class:: informark
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180
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181 **More information**
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182
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183 It is recommended that you refer to the ``RnaChipIntegrator``
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184 documentation for information on the contents of each output file:
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185
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186 * http://rnachipintegrator.readthedocs.org/en/latest/
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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 **Credits**
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193
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194 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
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195 University of Manchester. It runs the RnaChipIntegrator package which has also been
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196 developed by this group, and is documented at
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197 https://pypi.python.org/pypi/RnaChipIntegrator/
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198
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199 Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.
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200 </help>
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201 <expand macro="citations" />
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202 </tool>