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annotate sleuth.xml @ 1:d3e447dd52c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
author iuc
date Wed, 07 Jun 2023 11:47:30 +0000
parents 5f1cb4c28d73
children d6b5fc94062c
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5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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1 <tool id="sleuth" name="Sleuth" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@">
5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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2 <description>differential expression analysis</description>
5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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6 <expand macro='xrefs'/>
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7 <expand macro='requirements'/>
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8 <stdio>
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9 <regex match="Execution halted"
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10 source="both"
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11 level="fatal"
5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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12 description="Execution halted." />
5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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13 <regex match="Error in"
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14 source="both"
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15 level="fatal"
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16 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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17 <regex match="Fatal error"
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18 source="both"
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19 level="fatal"
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20 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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21 </stdio>
5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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22 <version_command><![CDATA[echo $(R --version | grep version | grep -v GNU)", sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")]]></version_command>
5f1cb4c28d73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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23 <command><![CDATA[
1
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24 #import os
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25 mkdir -p './kallisto_outputs' &&
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26 #set $cond_files = list()
1
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27 #if $experiment_design.selector == "single"
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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28 #set $factor_levels = list()
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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29 #set $cond_n_files = list()
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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30 #for $level in $experiment_design.rep_factorLevel
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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31 $factor_levels.append(str($level.factorLevel))
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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32 $cond_n_files.append(len(str($level.countsFile).split(",")))
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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33 #for $i, $count in enumerate(str($level.countsFile).split(","))
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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34 #set $fname = str($level.factorLevel) + "_" + str($i) + '.h5'
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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35 #set $output_path = "/".join(['./kallisto_outputs',$fname])
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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36 ln -s '${count}' $output_path &&
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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37 $cond_files.append($output_path)
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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38 #end for
0
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39 #end for
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40 #else
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41 #for $count in $experiment_design.countsFile
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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42 #set $output_path = "/".join(['./kallisto_outputs',$count.element_identifier])
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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43 ln -s '${count}' $output_path &&
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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44 $cond_files.append($output_path)
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45 #end for
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46 #end if
0
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47 Rscript '${__tool_directory__}/sleuth.R'
1
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48 #if $experiment_design.selector == "single"
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49 #for $i, $factor in enumerate($factor_levels)
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50 --factorLevel $factor
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51 --factorLevel_n $cond_n_files[$i]
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52 #end for
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53 #else
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54 --metadata_file $experiment_design.metadata_file
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55 #end if
0
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56 #for $file in $cond_files
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57 --factorLevel_counts $file
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58 #end for
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59 --cores \${GALAXY_SLOTS:-4}
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60 $advanced_options.normalization
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61 --nbins $advanced_options.nbins
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62 --lwr $advanced_options.lwr
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63 --upr $advanced_options.upr
1
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64 --experiment_design $experiment_design.selector
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65 ]]></command>
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66 <inputs>
1
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67 <conditional name="experiment_design">
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68 <param name="selector" type="select" label="Experiment design" help="If you have multiple experimental conditions, you should use propably the complex design mode. In the help section you can find more information.">
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69 <option value="single">Simple design mode (one experimental factor)</option>
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70 <option value="complex">Complex design mode (two experimental factors)</option>
0
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71 </param>
1
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72 <when value="single">
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73 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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74 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
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75 help="Only letters, numbers and underscores will be retained in this field">
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76 <sanitizer>
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77 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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78 </sanitizer>
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79 </param>
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80 <param name="countsFile" type="data" format="h5" multiple="true" label="Counts file(s)"/>
d3e447dd52c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6fbf73689708cfbdf3d9d783af4988bad7137f93
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81 </repeat>
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82 </when>
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83 <when value="complex">
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84 <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/>
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85 <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about it in the help section" />
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86 </when>
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87 </conditional>
0
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88 <section name="advanced_options" title="Advanced options" expanded="true">
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89 <param argument="normalization" type="boolean" truevalue="--normalize" falsevalue="" checked="true" label="Normalize data"
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90 help="If this is set to false, bootstraps will not be read and transformation of the data will not be done. This should
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91 only be set to false if one desires to do a quick check of the raw data. " />
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92 <param argument="nbins" type="integer" min="0" value="100" label="NBins" help="The number of bins that the data should be
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93 split for the sliding window shrinkage using the mean-variance curve." />
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94 <param argument="lwr" type="float" min="0" max="1" value="0.25" label="LWR" help="The lower range of variances within each
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95 bin that should be included for the shrinkage procedure. " />
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96 <param argument="upr" type="float" min="0" max="1" value="0.75" label="UPR" help="The upper range of variances within each
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97 bin that should be included for the shrinkage procedure." />
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98 </section>
1
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99
0
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100 </inputs>
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101 <outputs>
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102 <data name="sleuth_table" from_work_dir="sleuth_table.tab" format="tabular" label="${tool.name} on ${on_string}: DE table">
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103 <actions>
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104 <action name="column_names" type="metadata" default="target_id,pval,qval,test_stat,rss,degrees_free,mean_obs,var_obs,tech_var,sigma_sq,smooth_sigma_sq,final_sigma_sq" />
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105 </actions>
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106 </data>
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107 <data name="pca_plot" from_work_dir="pca_plot.pdf" format="pdf" label="${tool.name} on ${on_string}: PCA plot"/>
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108 <data name="density_plot" from_work_dir="group_density.pdf" format="pdf" label="${tool.name} on ${on_string}: density plot"/>
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109 </outputs>
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110 <tests>
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111 <test expect_num_outputs="3">
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112 <repeat name="rep_factorLevel">
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113 <param name="factorLevel" value="Control"/>
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114 <param name="countsFile" value="kallisto_output_01.h5,kallisto_output_02.h5"/>
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115 </repeat>
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116 <repeat name="rep_factorLevel">
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117 <param name="factorLevel" value="Cancer"/>
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118 <param name="countsFile" value="kallisto_output_03.h5,kallisto_output_04.h5"/>
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119 </repeat>
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120 <section name="advanced_options">
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121 <param name="normalization" value="true"/>
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122 <param name="nbins" value="100"/>
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123 <param name="lwr" value="0.25"/>
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124 <param name="upr" value="0.75"/>
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125 </section>
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126 <output name="sleuth_table" ftype="tabular">
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127 <assert_contents>
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128 <has_size value="689791" delta="100"/>
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129 <has_text text="ENST00000281092.9"/>
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130 <has_text text="ENST00000700211.1"/>
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131 </assert_contents>
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132 </output>
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133 <output name="pca_plot" file="test01_pca.pdf" ftype="pdf" compare="sim_size"/>
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134 <output name="density_plot" file="test01_density.pdf" ftype="pdf" compare="sim_size"/>
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135 </test>
1
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136 <test expect_num_outputs="3">
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137 <conditional name="experiment_design">
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138 <param name="selector" value="complex"/>
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139 <param name="countsFile">
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140 <collection type="list">
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141 <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/>
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142 <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/>
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143 <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/>
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144 <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/>
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145 </collection>
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146 </param>
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147 <param name="metadata_file" value="design.tab"/>
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148 </conditional>
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149 <section name="advanced_options">
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150 <param name="normalization" value="true"/>
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151 <param name="nbins" value="100"/>
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152 <param name="lwr" value="0.25"/>
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153 <param name="upr" value="0.75"/>
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154 </section>
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155 <output name="sleuth_table" ftype="tabular">
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156 <assert_contents>
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157 <has_size value="756310" delta="100"/>
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158 <has_text text="ENST00000394894.8"/>
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159 <has_text text="ENST00000524187.1"/>
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160 </assert_contents>
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161 </output>
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162 <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/>
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163 <output name="density_plot" file="test02_density.pdf" ftype="pdf" compare="sim_size"/>
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164 </test>
0
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165 </tests>
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166 <help><![CDATA[
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167
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168 .. class:: infomark
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169
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170 **Purpose**
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171
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172 Sleuth is a tool for the analysis and comparison of multiple related RNA-Seq experiments. Key features include:
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173
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174 - The ability to perform both transcript-level and gene-level analysis.
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175 - Compatibility with kallisto enabling a fast and accurate workflow from reads to results.
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176 - The use of bootstraps to ascertain and correct for technical variation in experiments.
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177 - An interactive app for exploratory data analysis.
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178
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179 To use sleuth, RNA-Seq data must first be quantified with kallisto, which is a program for very fast RNA-Seq quantification based on
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180 pseudo-alignment. An important feature of kallisto is that it outputs bootstraps along with the estimates of transcript abundances.
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181 These can serve as proxies for technical replicates, allowing for an ascertainment of the variability in estimates due to the random
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182 processes underlying RNA-Seq as well as the statistical procedure of read assignment.
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183
1
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184 .. class:: infomark
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185
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186 **Experimental design tabular input for complex experimental designs**
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187
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188 The experimental design input should have this format:
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189
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190 ::
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191
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192 data_filename condition sample
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193 finename_01.fastq.gz condition1 replicate1
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194 filename_02.fastq.gz condition1 replicate2
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195 filename_03.fastq.gz condition2 replicate1
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196 filename_04.fastq.gz condition2 replicate2
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197
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198
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199 The tabular file **requires to have the same column names** as the example (data_file, condition, sample). The data file column correspond to original FASTQ filenames uploaded to Galaxy.
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200 Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**.
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201
0
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202 ]]></help>
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203 <expand macro="citations" />
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204 </tool>