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annotate difftrans.xml @ 0:c34c364ce75d

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author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Tue, 21 Jul 2015 14:48:39 +0100
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1 <tool id="difftrans" name="Differential Translation Analysis" version="0.1.0">
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2 <description>
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3 (Step 4) Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
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4 translation analysis with baySeq.
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5 </description>
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6 <requirements>
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7 <requirement type="package" version="3.1.2">R</requirement>
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8 <requirement type="package" version="6.2">readline</requirement>
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9 <requirement type="package" version="2.3.10">rpy2</requirement>
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10 <requirement type="package" version="0.4.0">riboseqr_wrapper_deps
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11 </requirement>
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12 </requirements>
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13 <stdio>
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14 <exit_code range="1:" level="fatal" description="Error"/>
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15 </stdio>
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16 <command interpreter="python">riboseqr/difftrans.py
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17 --rdata_load "$rdata_load"
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18 --slice_lengths "$slice_lengths"
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19 --frames "$frames"
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20 --group1 "$group1"
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21 --group2 "$group2"
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22 --num_counts "$num_counts"
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23 --normalize "$normalize"
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24 --html_file "$html_file"
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25 --output_path "$html_file.files_path"
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26 </command>
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27 <inputs>
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28 <param name="rdata_load" format="rda" type="data"
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29 label="Select Metagene analysis (R data file)"
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30 multiple="false">
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31 <validator type="expression"
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32 message="Please check if the correct RDA file is selected">value.name == "Metagene analysis (R data file)"</validator>
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33 </param>
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34 <param name="slice_lengths" type="text"
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35 label="&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;Ribo and RNA counts (riboSeqR)&lt;/font&gt;&lt;/h4&gt;Lengths of ribosome footprints to inform count data"
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36 value="27,28">
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37 <validator type="empty_field" message="Field requires a value"/>
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38 </param>
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39 <param name="frames" type="text" label="Frames corresponding to the lengths of ribosome footprints given above"
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40 value="0,2">
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41 <validator type="empty_field" message="Field requires a value"/>
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42 </param>
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43 <param type="text" name="group1"
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44 label="&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;baySeq Analysis&lt;/font&gt;&lt;/h4&gt;Group (model) structure to test on the data"
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45 help="ex. 1,1,1,1">
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46 <validator type="empty_field" message="Field requires a value"/>
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47 </param>
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48 <param type="text" name="group2" label="and" help="ex. WT,WT,M,M">
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49 <validator type="empty_field" message="Field requires a value"/>
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50 </param>
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51 <param type="integer" name="num_counts"
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52 label="How many results to return? (top candidates for differential translation)"
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53 value="10"/>
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54
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55 <param name="normalize" type="boolean" checked="no"
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56 label="Normalize data?" falsevalue="FALSE" truevalue="TRUE"/>
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57 </inputs>
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58 <outputs>
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59 <data format="html" name="html_file"
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60 label="Differential Translation Analysis (HTML report)"/>
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61 </outputs>
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62 <!--<tests>-->
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63 <!--<test>-->
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64 <!--<param name="rdata_load" value="Metagene analysis (R data file)"/>-->
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65 <!--<param name="slice_lengths" value="27,28"/>-->
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66 <!--<param name="frames" value="0,2"/>-->
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67 <!--<param name="group1" value="1,1,1,1"/>-->
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68 <!--<param name="group2" value="WT,WT,M,M"/>-->
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69 <!--<param name="normalize" checked="yes"/>-->
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70 <!--<output name="html_file" file="Differential_Translation_Analysis_(HTML_report)">-->
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71 <!--<extra_files type="file" name="RNACounts.csv" value="RNACounts.csv" ftype="csv"/>-->
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72 <!--<extra_files type="file" name="RiboCounts.csv" value="RiboCounts.csv" ftype="csv"/>-->
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73 <!--<extra_files type="file" name="TopCounts.csv" value="TopCounts.csv" ftype="csv"/>-->
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74 <!--</output>-->
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75 <!--</test>-->
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76 <!--</tests>-->
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77 <help>
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78 Differential Translation Analysis
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79 ---------------------------------
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80 riboSeqR version: ``1.0.5``, baySeq version: ``2.0.50``.
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81
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82 This tool can be used for obtaining the Ribo and RNA-Seq counts and
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83 finding the
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84 top candidates for differential translation using baySeq. The input is
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85 the
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86 R data file from the Metagene analysis step.
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87
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88 How to use?
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89 -----------
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90 Inputs
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91 ......
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92 Select *Metagene analysis (R data file)*, enter lengths of ribosome
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93 footprints
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94 and the frames. For baySeq analysis, enter the group model and the
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95 number of
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96 results to return. Please refer to the documentation for explanation of
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97 the
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98 options.
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99
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100 Outputs
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101 .......
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102 The following files will be generated on completion:
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103
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104 *Differential Translation Analysis (HTML report)*
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105
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106 A HTML file with results, links to other output files and the R script
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107 used for
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108 the session.
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109
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110 riboSeqR functions used
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111 .......................
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112 ``sliceCounts``, ``rnaCounts``.
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113
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114 baySeq functions used
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115 .....................
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116 ``getLibsizes``, ``getPriors``, ``getLikelihoods``, ``topCounts``.
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117
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118 For detailed description of the functions and the options used, please
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119 consult
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120 the riboSeqR and baySeq documentation.
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121
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122 Links
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123 .....
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124 * `riboSeqR &lt;http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html&gt;`_
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125 * `baySeq &lt;http://bioconductor.org/packages/3.0/bioc/html/baySeq.html&gt;`_
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126 </help>
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127 <citations>
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128 <citation type="bibtex">
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129 @Manual{,
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130 title = {riboSeqR: Analysis of sequencing data from ribosome
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131 profiling experiments.},
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132 author = {Thomas J. Hardcastle},
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133 year = {2014},
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134 note = {R package version 1.0.5},
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135 }
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136 </citation>
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137 <citation type="bibtex">
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138 @Manual{,
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139 title = {baySeq: Empirical Bayesian analysis of patterns of
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140 differential
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141 expression in count data},
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142 author = {Thomas J. Hardcastle},
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143 year = {2012},
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144 note = {R package version 2.0.50},
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145 }
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146 </citation>
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147 <citation type="doi">10.1186/1471-2105-11-422</citation>
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148 </citations>
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149 </tool>