Mercurial > repos > iuc > ruvseq

annotate ruvseq.xml @ 3:d1f7fa5bb3cb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
author iuc
date Fri, 23 Jul 2021 22:37:45 +0000
parents fed9d0350d72
children 3a083c78896e
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fed9d0350d72 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
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1 <tool id="ruvseq" name="Remove Unwanted Variation" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">
0
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2 <description>from RNA-seq data</description>
2
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3 <macros>
3
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4 <token name="@TOOL_VERSION@">1.26.0</token>
d1f7fa5bb3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
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5 <token name="@WRAPPER_VERSION@">0</token>
2
fed9d0350d72 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
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6 </macros>
0
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">bioconductor-ruvseq</requirement>
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d1f7fa5bb3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
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9 <requirement type="package" version="1.32.0">bioconductor-deseq2</requirement>
d1f7fa5bb3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
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10 <requirement type="package" version="1.20.0">bioconductor-tximport</requirement>
d1f7fa5bb3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
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11 <requirement type="package" version="1.44.0">bioconductor-genomicfeatures</requirement>
d1f7fa5bb3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
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12 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
d1f7fa5bb3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
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13 <requirement type="package" version="1.20.3">r-getopt</requirement>
d1f7fa5bb3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
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14 <requirement type="package" version="1.4.4">r-reshape2</requirement>
0
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15 </requirements>
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16 <stdio>
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17 <regex match="Execution halted"
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18 source="both"
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19 level="fatal"
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20 description="Execution halted." />
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21 <regex match="Error in"
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22 source="both"
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23 level="fatal"
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24 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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25 <regex match="Fatal error"
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26 source="both"
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27 level="fatal"
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28 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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29 </stdio>
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30 <version_command><![CDATA[
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31 echo $(R --version | grep version | grep -v GNU)", RUVSeq version" $(R --vanilla --slave -e "library(RUVSeq); cat(sessionInfo()\$otherPkgs\$RUVSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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32 ]]></version_command>
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33 <command><![CDATA[
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34 #if $tximport.tximport_selector == 'tximport':
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35 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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36 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf &&
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37 #else:
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38 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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39 #end if
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40 #end if
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41
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42 Rscript '${__tool_directory__}/ruvseq.R'
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43 #if $pdf:
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44 -p '$plots'
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45 #end if
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46
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47 --sample_json '$sampleTable'
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48
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49 $header
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50
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51 --min_k $min_k
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52 --max_k $max_k
1
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53 --min_mean_count $min_mean_count
0
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54
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55 #if $tximport.tximport_selector == 'tximport':
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56 --txtype $tximport.txtype
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57 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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58 --tx2gene mapping.gtf
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59 #else:
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60 --tx2gene mapping.txt
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61 #end if
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62 #end if
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63 ]]></command>
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64 <configfiles>
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65 <configfile name="sampleTable">
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66 #import json
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67 #set sample_table = []
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68 #for $level in $rep_factorLevel:
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69 #for $file in $level.countsFile:
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70 #silent $sample_table.append({"path": str($file), "label": str($file.element_identifier), "condition": str($level.factorLevel)})
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71 #end for
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72 #end for
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73 #echo json.dumps($sample_table)
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74 </configfile>
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75 </configfiles>
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76 <inputs>
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77 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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78 <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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79 help="Only letters, numbers and underscores will be retained in this field">
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80 <sanitizer>
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81 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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82 </sanitizer>
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83 </param>
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84 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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85 </repeat>
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86 <param name="min_k" type="integer" value="1" min="1" label="Try to find at least this many factors of unwanted variation" />
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87 <param name="max_k" type="integer" value="1" min="1" label="Try to find at most this many factors of unwanted variation" />
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88 <param name="min_mean_count" type="integer" value="5" min="0" label="Ignore genes with fewer than this many counts on average" />
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89 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />
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90
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91 <conditional name="tximport">
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92 <param name="tximport_selector" type="select" label="Choice of Input data">
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93 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
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94 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
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95 </param>
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96 <when value="tximport">
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97 <param name="txtype" type="select" label="Program used to generate TPMs">
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98 <option value="kallisto">kallisto</option>
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99 <option value="sailfish">Sailfish</option>
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100 <option value="salmon">Salmon</option>
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101 </param>
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102 <conditional name="mapping_format">
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103 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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104 <option value="gtf" selected="True">GTF</option>
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105 <option value="tabular">Transcript-ID and Gene-ID mapping file</option>
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106 </param>
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107 <when value="gtf">
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108 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/>
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109 </when>
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110 <when value="tabular">
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111 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>
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112 </when>
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113 </conditional>
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114 </when>
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115 <when value="count" />
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116 </conditional>
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117 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
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118 label="Visualising the analysis results"
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119 help="output an additional PDF files" />
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120 </inputs>
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121 <outputs>
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122 <collection name="unwanted_variation" type="list" label="RUVSeq covariate files on ${on_string}">
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123 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="." visible="false"/>
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124 </collection>
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125 <data format="pdf" name="plots" label="RUVSeq diagonstic plots on ${on_string}">
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126 <filter>pdf == True</filter>
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127 </data>
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128 </outputs>
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129 <tests>
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130 <!--Ensure counts files with header works -->
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131 <test>
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132 <repeat name="rep_factorLevel">
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133 <param name="factorLevel" value="Treated"/>
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134 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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135 </repeat>
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136 <repeat name="rep_factorLevel">
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137 <param name="factorLevel" value="Untreated"/>
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138 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
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139 </repeat>
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140 <param name="pdf" value="true"/>
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141 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/>
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142 <output_collection name="unwanted_variation" type="list">
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143 <element name="batch_effects_control_method_k1">
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144 <assert_contents>
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145 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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146 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
0
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147 </assert_contents>
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148 </element>
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149 <element name="batch_effects_replicate_method_k1">
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150 <assert_contents>
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151 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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152 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
0
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153 </assert_contents>
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154 </element>
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155 <element name="batch_effects_residual_method_k1">
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156 <assert_contents>
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157 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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158 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
0
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159 </assert_contents>
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160 </element>
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161 </output_collection>
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162 </test>
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163 <!--Ensure counts files without header works -->
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164 <test>
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165 <repeat name="rep_factorLevel">
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166 <param name="factorLevel" value="Treated"/>
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167 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
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168 </repeat>
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169 <repeat name="rep_factorLevel">
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170 <param name="factorLevel" value="Untreated"/>
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171 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
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172 </repeat>
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173 <param name="pdf" value="true"/>
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174 <param name="header" value="false"/>
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175 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/>
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176 <output_collection name="unwanted_variation" type="list">
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177 <element name="batch_effects_control_method_k1">
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178 <assert_contents>
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179 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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180 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
0
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181 </assert_contents>
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182 </element>
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183 <element name="batch_effects_replicate_method_k1">
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184 <assert_contents>
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185 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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186 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
0
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187 </assert_contents>
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188 </element>
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189 <element name="batch_effects_residual_method_k1">
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190 <assert_contents>
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191 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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192 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/>
0
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193 </assert_contents>
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194 </element>
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195 </output_collection>
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196 </test>
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197 <!--Ensure sailfish files work -->
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198 <test>
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199 <repeat name="rep_factorLevel">
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200 <param name="factorLevel" value="Treated"/>
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201 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
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202 </repeat>
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203 <repeat name="rep_factorLevel">
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204 <param name="factorLevel" value="Untreated"/>
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205 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
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206 </repeat>
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207 <param name="pdf" value="true"/>
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208 <param name="tximport_selector" value="tximport"/>
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209 <param name="txtype" value="sailfish"/>
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210 <param name="mapping_format_selector" value="tabular"/>
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211 <param name="tabular_file" value="tx2gene.tab"/>
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212 <param name="min_mean_count" value="0"/>
0
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213 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/>
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214 <output_collection name="unwanted_variation" type="list">
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215 <element name="batch_effects_control_method_k1">
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216 <assert_contents>
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217 <has_text_matching expression="identifier\tcondition\tW_1"/>
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218 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
0
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219 </assert_contents>
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220 </element>
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221 <element name="batch_effects_replicate_method_k1">
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222 <assert_contents>
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223 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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224 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
0
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225 </assert_contents>
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226 </element>
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227 <element name="batch_effects_residual_method_k1">
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228 <assert_contents>
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229 <has_text_matching expression="identifier\tcondition\tW_1"/>
1
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230 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
0
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231 </assert_contents>
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232 </element>
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233 </output_collection>
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234 </test>
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235 </tests>
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236 <help><![CDATA[
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237 .. class:: infomark
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238
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239 **What it does**
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240
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241 RUVSeq normalizes RNA-seq data using factor analysis of control genes or samples. RUVSeq has been designed for detecting unwanted variation using replicate sample information. The current RUVSeq Galaxy tool only implements estimating unwanted variation for primary factors.
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242 RUVSeq implements 3 different methods for the estimation of unwanted variation:
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243
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244 RUVg estimates the factors of unwanted variation using control genes
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245
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246 RUVs estimates the factors of unwanted variation using replicate samples
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247
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248 RUVr estimating the factors of unwanted variation using residuals.
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249
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250 This tool runs all RUV methods and outputs diagnostic plots and tables with covariates that
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251 may be used for differential expression analsys.
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252
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253 -----
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254
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255 **Inputs**
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256
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257 **Count Files**
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258
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259 RUVSeq_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No.
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260
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261 RUVSeq_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2.
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262
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263 **Salmon or Sailfish Files**
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264
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265 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below.
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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266
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267 Example:
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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268
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269 ============ ========== =============== =========== ===========
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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270 Name Length EffectiveLength TPM NumReads
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271 ------------ ---------- --------------- ----------- -----------
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272 NR_001526 164 20.4518 0 0
61dffb20b6f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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273 NR_001526_1 164 20.4518 0 0
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274 NR_001526_2 164 20.4518 0 0
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275 NM_130786 1764 1956.04 2.47415 109.165
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276 NR_015380 2129 2139.53 1.77331 85.5821
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277 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
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278 NM_001198819 9527 7964.62 0 0
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279 NM_001198820 9410 7855.78 0 0
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280 NM_014576 9267 7714.88 0.0481114 8.37255
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281 ============ ========== =============== =========== ===========
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282
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283 **kallisto Files**
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284
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285 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
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286
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287 Example:
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288
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289 ============ ========== =============== =========== ===========
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290 target_id length eff_length est_counts tpm
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291 ------------ ---------- --------------- ----------- -----------
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292 NR_001526 164 20.4518 0 0
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293 NR_001526_1 164 20.4518 0 0
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294 NR_001526_2 164 20.4518 0 0
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295 NM_130786 1764 1956.04 109.165 2.47415
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296 NR_015380 2129 2139.53 85.5821 1.77331
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297 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
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298 NM_001198819 9527 7964.62 0 0
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299 NM_001198820 9410 7855.78 0 0
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300 NM_014576 9267 7714.88 8.37255 0.0481114
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301 ============ ========== =============== =========== ===========
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302
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303 -----
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304
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305 **Output**
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306
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307 RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF.
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308
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309 .. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html
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310 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
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311 ]]></help>
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312 <citations>
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313 <citation type="doi">10.1038/nbt.2931</citation>
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314 </citations>
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315 </tool>