Mercurial > repos > devteam > cuffdiff

annotate cuffdiff_wrapper.xml @ 6:986b6cbd0f59 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
author iuc
date Mon, 06 Jul 2020 18:19:14 +0000
parents 3d8071386667
children 456797205473
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986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
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1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.6">
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2 <description>find significant changes in transcript expression, splicing, and promoter use</description>
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3 <macros>
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4 <import>cuff_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
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8 </expand>
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9 <version_command><![CDATA[cuffdiff 2>&1 | head -n 1]]></version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 cuffdiff
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12 --no-update-check
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13 --quiet
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14 --FDR=$fdr
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15 --num-threads="\${GALAXY_SLOTS:-4}"
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16 --min-alignment-count=$min_alignment_count
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17 --library-norm-method=$library_norm_method
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18 --dispersion-method=$dispersion_method
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19
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20 ## Set advanced SE data parameters?
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21 #if $additional.sAdditional == "Yes":
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22 -m $additional.frag_mean_len
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23 -s $additional.frag_len_std_dev
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24 #end if
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25
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26 ## Multi-read correct?
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27 #if $multiread_correct :
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28 -u
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29 #end if
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30
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31 ## Bias correction?
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32 #if $bias_correction.do_bias_correction == "Yes":
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33 -b
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34 #if $bias_correction.seq_source.index_source == "history":
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35 ## Custom genome from history.
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36 '$bias_correction.seq_source.ref_file'
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37 #else:
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38 ## Built-in genome.
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39 '${bias_correction.seq_source.index.fields.path}'
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40 #end if
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41 #end if
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42
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43 @CONDITION_LABELS@
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44
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45 $length_correction
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46
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47 ## Set advanced parameters for cufflinks
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48 #if $advanced_settings.sAdvanced == "Yes":
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49 #if str($advanced_settings.library_type) != 'auto':
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50 --library-type=$advanced_settings.library_type
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51 #end if
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52 #if $advanced_settings.mask_file:
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53 --mask-file '$advanced_settings.mask_file'
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54 #end if
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55 #if $advanced_settings.time_series:
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56 --time-series
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57 #end if
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58 --max-mle-iterations=$advanced_settings.max_mle_iterations
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59 $advanced_settings.hits_norm
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60 --max-bundle-frags=$advanced_settings.max_bundle_frags
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61 --num-frag-count-draws=$advanced_settings.num_frag_count_draws
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62 --num-frag-assign-draws=$advanced_settings.num_frag_assign_draws
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63 --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test
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64 #end if
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65 ## Inputs.
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66 '$gtf_input'
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67
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68 @CONDITION_SAMPLES@
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69 #if $generate_sqlite:
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70 &&
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71 Rscript '$__tool_directory__/cummeRbund.R'
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72 #end if
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73 ]]>
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74 </command>
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75 <inputs>
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76 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
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77 <param name="omit_tabular_output" type="boolean" truevalue="yes" falsevalue="no" label="Omit Tabular Datasets" help="Discard the tabular output." />
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78 <param name="generate_sqlite" type="boolean" truevalue="yes" falsevalue="no" label="Generate SQLite" help="Generate a SQLite database for use with cummeRbund." />
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79 <expand macro="condition_inputs" />
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80 <param name="library_norm_method" type="select" label="Library normalization method">
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81 <option value="geometric" selected="True">geometric</option>
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82 <option value="classic-fpkm">classic-fpkm</option>
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83 <option value="quartile">quartile</option>
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84 </param>
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85
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86 <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'">
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87 <option value="pooled" selected="True">pooled</option>
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88 <option value="per-condition">per-condition</option>
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89 <option value="blind">blind</option>
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90 <option value="poisson">poisson</option>
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91 </param>
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92
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93 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
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94 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count"
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95 help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
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96 <param name="multiread_correct" type="boolean" label="Use multi-read correct"
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97 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." />
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98
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99 <conditional name="bias_correction">
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100 <param name="do_bias_correction" type="select" label="Perform Bias Correction"
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101 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
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102 <option value="No">No</option>
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103 <option value="Yes">Yes</option>
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104 </param>
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105 <when value="Yes">
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106 <conditional name="seq_source">
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107 <param name="index_source" type="select" label="Reference sequence data">
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108 <option value="cached">Locally cached</option>
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109 <option value="history">History</option>
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110 </param>
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111 <when value="cached">
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112 <param name="index" type="select" label="Using reference genome">
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113 <options from_data_table="fasta_indexes">
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114 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
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115 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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116 </options>
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117 </param>
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118 </when>
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119 <when value="history">
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120 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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121 </when>
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122 </conditional>
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123 </when>
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124 <when value="No"></when>
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125 </conditional>
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126
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127 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
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128 <option value="No" selected="true">No</option>
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129 <option value="Yes">Yes</option>
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130 </param>
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131
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132 <param name="include_count_files" type="select" label="Include Count Based output files"
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133 help="Cuffdiff estimates the number of fragments that originated from each transcript, primary transcript, and gene in each sample. Primary transcript and gene counts are computed by summing the counts of transcripts in each primary transcript group or gene group.">
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134 <option value="No" selected="true">No</option>
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135 <option value="Yes">Yes</option>
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136 </param>
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137
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138 <param name="length_correction" type="select" label="apply length correction" help="mode of length normalization to transcript fpkm.">
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139 <option value="" selected="true">cufflinks effective length correction</option>
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140 <option value="--no-effective-length-correction">standard length correction</option>
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141 <option value="--no-length-correction">no length correction at all (use raw counts)</option>
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142 </param>
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143
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144 <conditional name="additional">
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145 <param name="sAdditional" type="select" label="Set Additional Parameters for single end reads? (not recommended for paired-end reads)">
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146 <option value="No" selected="True">No</option>
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147 <option value="Yes">Yes</option>
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148 </param>
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149 <when value="No"></when>
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150 <when value="Yes">
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151 <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
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152 <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
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153 </when>
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154 </conditional>
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155
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156 <conditional name="advanced_settings">
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157 <param name="sAdvanced" type="select" label="Set Advanced Cuffdiff parameters? ">
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158 <option value="No" selected="True">No</option>
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159 <option value="Yes">Yes</option>
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160 </param>
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161 <when value="No"></when>
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162 <when value="Yes">
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163 <param type="select" name="library_type" label="Library prep used for input reads" help="">
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164 <option value="auto" selected="True">Auto Detect</option>
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165 <option value="ff-firststrand">ff-firststrand</option>
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166 <option value="ff-secondstrand">ff-secondstrand</option>
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167 <option value="ff-unstranded">ff-unstranded</option>
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168 <option value="fr-firststrand">fr-firststrand</option>
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169 <option value="fr-secondstrand">fr-secondstrand</option>
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170 <option value="fr-unstranded" >fr-unstranded</option>
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171 <option value="transfrags">transfrags</option>
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172 </param>
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173 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" />
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174 <param name="time_series" type="boolean" label="Perform Time Series analysis"
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175 help="Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)" />
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176 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
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177 <param name="hits_norm" type="select" label="Hits included in normalization" help="All Hits: With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. Compatible Hits: With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. It is active by default." >
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178 <option value="--compatible-hits-norm" selected="True">Compatible Hits</option>
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179 <option value="--total-hits-norm">All Hits</option>
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180 </param>
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181 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
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182 help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" />
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183 <param name="num_frag_count_draws" type="integer" value="100" label="Number of fragment generation samples"
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184 help="Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 100."/>
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185 <param name="num_frag_assign_draws" type="integer" value="50" label="Number of fragment assignment samples per generation" help="For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 50."/>
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186 <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." />
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187 </when>
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188 </conditional>
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189 </inputs>
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190 <outputs>
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191 <!-- Optional read group datasets. -->
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192 <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
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193 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
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194 </data>
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195 <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
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196 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
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197 </data>
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198 <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
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199 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
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200 </data>
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201 <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
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202 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
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203 </data>
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204 <data format="txt" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
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205 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
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206 </data>
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207 <data format="txt" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
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208 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
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209 </data>
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210 <!-- Standard datasets. -->
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211 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff">
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212 <filter>not omit_tabular_output</filter>
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213 </data>
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214 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff">
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215 <filter>not omit_tabular_output</filter>
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216 </data>
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217 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff">
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218 <filter>not omit_tabular_output</filter>
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219 </data>
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220 <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff">
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221 <filter>not omit_tabular_output</filter>
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222 </data>
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223 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking">
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224 <filter>not omit_tabular_output</filter>
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225 </data>
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226 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
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227 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
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228 </data>
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229
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230 <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff">
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231 <filter>not omit_tabular_output</filter>
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232 </data>
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233 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking">
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234 <filter>not omit_tabular_output</filter>
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235 </data>
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236 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
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237 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
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238 </data>
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239
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240 <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff">
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241 <filter>not omit_tabular_output</filter>
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242 </data>
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243 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking">
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244 <filter>not omit_tabular_output</filter>
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245 </data>
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246 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
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9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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247 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
0
9a9e3e83889b Uploaded
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248 </data>
9a9e3e83889b Uploaded
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249
1
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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diff changeset
250 <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff">
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
251 <filter>not omit_tabular_output</filter>
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
252 </data>
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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253 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking">
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
254 <filter>not omit_tabular_output</filter>
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
255 </data>
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
256 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking">
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
257 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
258 </data>
6
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
259 <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" from_work_dir="cummeRbund.sqlite">
1
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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260 <filter>generate_sqlite</filter>
0
9a9e3e83889b Uploaded
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261 </data>
9a9e3e83889b Uploaded
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262 </outputs>
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263
9a9e3e83889b Uploaded
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264 <tests>
9a9e3e83889b Uploaded
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265 <test>
6
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
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266 <!--
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
267 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
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268 -->
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
269 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
270 <param name="generate_sqlite" value="yes" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
271 <param name="omit_tabular_output" value="yes" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
272 <conditional name="in_type">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
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273 <param name="set_in_type" value="BAM" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
274 <repeat name="conditions">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
275 <param name="name" value="q1" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
276 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
277 </repeat>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
278 <repeat name="conditions">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
279 <param name="name" value="q2" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
280 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
281 </repeat>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
282 </conditional>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
283 <param name="fdr" value="0.05" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
284 <param name="min_alignment_count" value="0" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
285 <param name="do_bias_correction" value="No" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
286 <param name="do_normalization" value="No" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
287 <param name="multiread_correct" value="No"/>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
288 <param name="sAdditional" value="No"/>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
289 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
1
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
290 </test>
9ba750f285e3 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
291 <test>
6
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
292 <!--
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
293 Use a list collection as conditions input
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
294 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
295 -->
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
296 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
297 <param name="generate_sqlite" value="yes" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
298 <param name="omit_tabular_output" value="yes" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
299 <conditional name="in_type">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
300 <param name="set_in_type" value="CONDITION_LIST" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
301 <param name="conditions">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
302 <collection type="list">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
303 <element name="q1" value="cuffdiff_in1.sam" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
304 <element name="q2" value="cuffdiff_in2.sam" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
305 </collection>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
306 </param>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
307 </conditional>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
308 <param name="fdr" value="0.05" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
309 <param name="min_alignment_count" value="0" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
310 <param name="do_bias_correction" value="No" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
311 <param name="do_normalization" value="No" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
312 <param name="multiread_correct" value="No"/>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
313 <param name="sAdditional" value="No"/>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
314 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
315 </test>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
316 <test>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
317 <!--
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
318 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
319 -->
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
320 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
321 <param name="omit_tabular_output" value="no" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
322 <conditional name="in_type">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
323 <param name="set_in_type" value="BAM" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
324 <repeat name="conditions">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
325 <param name="name" value="q1" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
326 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
327 </repeat>
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
328 <repeat name="conditions">
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
parents: 5
diff changeset
329 <param name="name" value="q2" />
986b6cbd0f59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
iuc
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330 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
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331 </repeat>
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332 </conditional>
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333 <param name="fdr" value="0.05" />
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334 <param name="min_alignment_count" value="0" />
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335 <param name="do_bias_correction" value="No" />
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336 <param name="do_normalization" value="No" />
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337 <param name="multiread_correct" value="No"/>
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338 <param name="sAdditional" value="No"/>
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339 <output name="splicing_diff" file="splicing.diff"/>
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340 <output name="promoters_diff" file="promoters.diff"/>
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341 <output name="cds_diff" file="cds.diff"/>
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342 <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/>
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343 <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/>
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344 <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/>
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345 <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/>
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346 <output name="genes_exp" file="genes.exp" lines_diff="200"/>
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347 <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/>
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348 <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/>
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349 <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/>
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350 </test>
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351 </tests>
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352 <help>
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353 **Cuffdiff Overview**
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354
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355 Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
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356
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357 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
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358
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359 ------
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360
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361 **Know what you are doing**
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362
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363 .. class:: warningmark
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364
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365 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
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366
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367 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
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368
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369 ------
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370
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371 **Input format**
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372
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373 Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
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374
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375 ------
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376
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377 **Outputs**
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378
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379 Cuffdiff produces many output files:
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380
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381 1. Transcript FPKM (+count) expression tracking.
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382 2. Gene FPKM (+count) expression tracking; tracks the summed FPKM of transcripts sharing each gene_id
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383 3. Primary transcript FPKM (+count) tracking; tracks the summed FPKM of transcripts sharing each tss_id
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384 4. Coding sequence FPKM (+count) tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id
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385 5. Transcript differential FPKM.
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386 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id
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387 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id
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388 8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id
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389 9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file.
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390 10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here.
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391 11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here.
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392
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393 -------
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394
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395 **Settings**
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396
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397 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.
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398
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399 ------
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400
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401 **Cuffdiff parameter list**
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402
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403 This is a list of implemented Cuffdiff options::
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404
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405 -m INT Average fragment length (SE reads); default 200
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406 -s INT Fragment legnth standard deviation (SE reads); default 80
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407 -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).
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408 --FDR FLOAT The allowed false discovery rate. The default is 0.05.
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409 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000
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410 --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile
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411 --dispersion-method Dispersion estimation method : Pooled (default), per-condition, blind, poisson
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412 -u Multi read correction tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.
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413 -b ref.fasta bias correction. Bias detection and correction can significantly improve accuracy of transcript abundance estimates.
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414 --no-effective-length-correction Use standard length correction
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415 --no-length-correction Disable all length correction.
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416 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
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417 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file
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418 --time-series Treat provided sam files as time series
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419 --compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.
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420 --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator
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421 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
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422 --num-frag-count-draws Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts.
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423 --num-frag-assign-draws For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts.
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424 --min-reps-for-js-test Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates.
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425 </help>
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426 <expand macro="citations"/>
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427 </tool>