| Previous changeset 21:a6fc9228e1a0 (2019-01-28) Next changeset 23:0696db066a5b (2019-03-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862 |
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modified:
deseq2.xml |
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added:
deseq2_macros.xml |
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| diff -r a6fc9228e1a0 -r e5c8afac22a7 deseq2.xml --- a/deseq2.xml Mon Jan 28 12:04:08 2019 -0500 +++ b/deseq2.xml Mon Feb 04 16:45:12 2019 -0500 |
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| @@ -1,11 +1,14 @@ -<tool id="deseq2" name="DESeq2" version="2.11.40.5"> +<tool id="deseq2" name="DESeq2" version="2.11.40.6"> <description>Determines differentially expressed features from count tables</description> + <macros> + <import>deseq2_macros.xml</import> + </macros> <requirements> - <requirement type="package" version="1.20.0">bioconductor-deseq2</requirement> + <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement> <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 --> - <requirement type="package" version="2.24.0">bioconductor-rhdf5</requirement> - <requirement type="package" version="1.8.0">bioconductor-tximport</requirement> - <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement> + <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement> + <requirement type="package" version="1.10.0">bioconductor-tximport</requirement> + <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement> <requirement type="package" version="1.20.2">r-getopt</requirement> <requirement type="package" version="0.8.0">r-ggrepel</requirement> <requirement type="package" version="3.0.1">r-gplots</requirement> @@ -57,14 +60,23 @@ #end if #set $filename_to_element_identifiers = {} #set $temp_factor_names = list() - #for $factor in $rep_factorName: + #for $factor in $select_data.rep_factorName: #set $temp_factor = list() #for $level in $factor.rep_factorLevel: #set $count_files = list() - #for $file in $level.countsFile: - $count_files.append(str($file)) - $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) - #end for + #if $select_data.how == 'group_tags': + #for $group in $level.groups.value: + #for $file in $select_data.countsFile.get_datasets_for_group($group): + $count_files.append(str($file)) + $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) + #end for + #end for + #else: + #for $file in $level.countsFile: + $count_files.append(str($file)) + $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) + #end for + #end if $temp_factor.append( {str($level.factorLevel): $count_files} ) #end for $temp_factor.reverse() @@ -106,23 +118,24 @@ #end if ]]></command> <inputs> - <repeat name="rep_factorName" title="Factor" min="1"> - <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> + <conditional name="select_data"> + <param name="how" type="select"> + <option value="datasets_per_level">Select datasets per level</option> + <option value="group_tags">Select group tags corresponding to levels</option> </param> - <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> - <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> - </repeat> - </repeat> + <when value="group_tags"> + <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/> + <expand macro="factor_repeat"> + <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/> + </expand> + </when> + <when value="datasets_per_level"> + <expand macro="factor_repeat"> + <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> + </expand> + </when> + </conditional> + <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/> <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" /> @@ -397,6 +410,41 @@ </assert_contents> </output> </test> + <!--Ensure group tags can be used to select factor levels --> + <test expect_num_outputs="1"> + <param name="select_data|how" value="group_tags"/> + <param name="select_data|countsFile"> + <collection type="list"> + <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/> + <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/> + <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/> + <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/> + <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/> + <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/> + </collection> + </param> + <repeat name="rep_factorName"> + <param name="factorName" value="Treatment"/> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Treated"/> + <param name="groups" value="primary:treated"/> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Untreated"/> + <param name="groups" value="primary:untreated"/> + </repeat> + </repeat> + <param name="pdf" value="False"/> + <param name="tximport_selector" value="tximport"/> + <param name="txtype" value="sailfish"/> + <param name="mapping_format_selector" value="tabular"/> + <param name="tabular_file" value="tx2gene.tab"/> + <output name="deseq_out" > + <assert_contents> + <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark |
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| diff -r a6fc9228e1a0 -r e5c8afac22a7 deseq2_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2_macros.xml Mon Feb 04 16:45:12 2019 -0500 |
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| @@ -0,0 +1,21 @@ +<macros> + <xml name="factor_repeat"> + <repeat name="rep_factorName" title="Factor" min="1"> + <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> + <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <yield/> + </repeat> + </repeat> + </xml> +</macros> \ No newline at end of file |