Mercurial > repos > iuc > sleuth

comparison sleuth.xml @ 1:d3e447dd52c8 draft

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