Mercurial > repos > sblanck > mpagenomics
changeset 5:4f753bb8681e draft
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
| author | sblanck |
|---|---|
| date | Tue, 20 Apr 2021 13:11:24 +0000 |
| parents | 3fcbb8030fcc |
| children | 7076911e5c64 |
| files | datatypes_conf.xml extractCN.xml filter.xml preprocess.xml segmentation.xml selectionExtracted.xml |
| diffstat | 6 files changed, 87 insertions(+), 58 deletions(-) [+] |
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--- a/datatypes_conf.xml Mon Apr 12 14:47:09 2021 +0000 +++ b/datatypes_conf.xml Tue Apr 20 13:11:24 2021 +0000 @@ -13,6 +13,8 @@ <datatype extension="sar" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="false"/> <!-- signal extraction file--> <datatype extension="sef" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/> + <datatype extension="saf" type="galaxy.datatypes.tabular:Tabular" subclass="true" display_in_upload="true"/> + <datatype extension="nzip" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/> <!--End MPAgenomics extensions--> </registration> </datatypes>
--- a/extractCN.xml Mon Apr 12 14:47:09 2021 +0000 +++ b/extractCN.xml Tue Apr 20 13:11:24 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="extract" name="Extract" version="1.2.0"> +<tool id="extract" name="Extract" version="1.3.0"> <description>copy number or allele B fraction signal</description> <requirements> <container type="docker">sblanck/mpagenomicsdependencies</container> @@ -10,8 +10,6 @@ --chrom '$chrom' --input '$input' --zip '$zip' - --output '$output' - --new_file_path '$output.extra_files_path' #if $settings.settingsType == "file": --settings_type '$settings.inputs' #end if @@ -19,11 +17,15 @@ --settings_type 'dataset' #end if #if $settingsSNP.signal == "fracB": - --settings_snp 'TRUE' + --new_file_path '$outputF.extra_files_path' + --output '$outputF' + --settings_snp 'TRUE' --settings_tumor '$settingsSNP.tumorcsvFracBsym' --symmetrize 'TRUE' #else - --settings_snp '$settingsSNP.snp' + --new_file_path '$outputC.extra_files_path' + --output '$outputC' + --settings_snp '$settingsSNP.snp' #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard": --settings_tumor 'None' #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor": @@ -38,7 +40,7 @@ </command> <inputs> <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/> - <param name="zip" type="data" format="zip" label="Zip results file" help="Zip results file generated by the Data normalization tool"/> + <param name="zip" type="data" format="nzip" label="Zip results file" help="Zip results file generated by the Data normalization tool"/> <conditional name="settings"> <param name="settingsType" type="select" label="Files selection Mode" help="Select the whole cel files dataset or pick-up only few files from the dataset"> <option value="dataset">Select whole dataset</option> @@ -138,7 +140,14 @@ </param> </inputs> <outputs> - <data format="sef" name="output" label="signal extraction of ${settingsSNP.signal} of ${input.name}" /> + <data format="saf" name="outputF" label="signal extraction of ${settingsSNP.signal} of ${input.name}"> + <filter>settingsSNP['signal']=='fracB'</filter> + </data> + + <data format="sef" name="outputC" label="signal extraction of ${settingsSNP.signal} of ${input.name}"> + <filter>settingsSNP['signal']=='CN'</filter> + </data> + <data format="log" name="log" label="log of signal extraction of ${settingsSNP.signal} of ${input.name}"> <filter>outputlog == "TRUE"</filter> </data>
--- a/filter.xml Mon Apr 12 14:47:09 2021 +0000 +++ b/filter.xml Tue Apr 20 13:11:24 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="callfilter" name="Filter" description="segmented and called data" version="1.2.0"> +<tool id="callfilter" name="Filter" description="segmented and called data" version="1.3.0"> <requirements> <container type="docker">sblanck/mpagenomicsdependencies</container> </requirements> @@ -6,43 +6,50 @@ <![CDATA[ Rscript ${__tool_directory__}/filter.R - --input '$input' + --input '${settingsSNP.input_cond}' --length '$length' --probes '$probes' - --new_file_path '$output.extra_files_path' #if $settingsSNP.signal == "fracB": - --nbcall 'normal' - #else + --nbcall 'normal' + --output '$outputF' + --new_file_path '$outputF.extra_files_path' + #else --nbcall '${settingsSNP.nbcall}' + --output '$outputC' + --new_file_path '$outputC.extra_files_path' #end if --settings_signal '$settingsSNP.signal' - --output '$output' --outputlog '$outputlog' --log '$log' ]]> </command> <inputs> - <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/> - <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/> - <param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/> - - <conditional name="settingsSNP"> + <conditional name="settingsSNP"> <param name="signal" type="select" multiple="false" label="Signal you want to work on"> <option value="CN">CN</option> <option value="fracB">fracB</option> </param> <when value="CN"> - <param name="nbcall" type="select" multiple="true" label="Label(s) to keep"> - <option value="double_loss">double loss</option> - <option value="loss">loss</option> - <option value="normal">normal</option> - <option value="gain">gain</option> - <option value="amplification">amplification</option> - </param> - </when> + <param name="input_cond" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/> + <param name="nbcall" type="select" multiple="true" label="Label(s) to keep"> + <option value="double_loss">double loss</option> + <option value="loss">loss</option> + <option value="normal">normal</option> + <option value="gain">gain</option> + <option value="amplification">amplification</option> + </param> + </when> + <when value="fracB"> + <param name="input_cond" type="data" format="sar" label="Segmented allele b data file" help="Input file with segments"/> + </when> </conditional> + + + <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/> + <param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/> + <param name="outputlog" type="select" label="Output log"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> @@ -50,9 +57,13 @@ </inputs> <outputs> - <data format="tabular" name="output" label="filter of ${on_string}" /> - - <data format="log" name="log" label="log of filter of ${input.name}"> + <data format="scr" name="outputC" label="filter of ${settingsSNP.input_cond.name}"> + <filter>settingsSNP['signal'] == 'CN'</filter> + </data> + <data format="sar" name="outputF" label="filter of ${settingsSNP.input_cond.name}"> + <filter>settingsSNP['signal'] == "fracB"</filter> + </data> + <data format="log" name="log" label="log of filter of ${settingsSNP.input_cond.name}"> <filter>outputlog == "TRUE"</filter> </data> </outputs>
--- a/preprocess.xml Mon Apr 12 14:47:09 2021 +0000 +++ b/preprocess.xml Tue Apr 20 13:11:24 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="preprocess" name="Data Normalization" version="1.2.0"> +<tool id="preprocess" name="Data Normalization" version="1.3.0"> <requirements> <container type="docker">sblanck/mpagenomicsdependencies</container> </requirements> @@ -72,7 +72,7 @@ doesn't occur. --> <data format="dsf" name="summary" label="Dataset summary file of ${datasetName}" /> - <data format="zip" name="zipresults" label="Results of normalization of ${datasetName}"/> + <data format="nzip" name="zipresults" label="Results of normalization of ${datasetName}"/> <data format="zip" name="zipfigures" label="Figures of normalization of ${datasetName}"> <filter>outputgraph == "TRUE"</filter> </data>
--- a/segmentation.xml Mon Apr 12 14:47:09 2021 +0000 +++ b/segmentation.xml Tue Apr 20 13:11:24 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="segmentation" name="Segmentation and calling" version="1.2.0"> +<tool id="segmentation" name="Segmentation and calling" version="1.3.0"> <description>of a previously normalized signal</description> <requirements> <container type="docker">sblanck/mpagenomicsdependencies</container> @@ -7,42 +7,39 @@ <![CDATA[ Rscript ${__tool_directory__}/segmentation.R - #if $signalType.signal == "CN": - --nbcall '$signalType.nbcall' - --cellularity '$signalType.cellularity' - #else + #if $input.signal == "CN": + --nbcall '$input.nbcall' + --cellularity '$input.cellularity' + --output '$outputC' + --new_file_path '$outputC.extra_files_path' + #else --nbcall '3' --cellularity '1.0' - #end if - --input '$input' - --new_file_path '$output.extra_files_path' + --output '$outputF' + --new_file_path '$outputF.extra_files_path' + #end if + --input '$input.input_cond' --outputlog '$outputlog' - --output '$output' --log '$log' --outputgraph '$outputgraph' --graph '$graph' --method '$method' - --signalType '$signalType.signal' + --signalType '$input.signal' --user_id '$__user_id__' ]]> </command> <inputs> - <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/> - - <param name="method" type="select" label="Segmentation method" help=""> - <option value="cghseg">cghseg</option> - <option value="PELT">PELT</option> - </param> - - <conditional name="signalType"> + <conditional name="input"> <param name="signal" type="select" multiple="false" label="Signal type"> <option value="CN">CN</option> <option value="fracB">fracB</option> </param> - <when value="fracB"/> + <when value="fracB"> + <param name="input_cond" type="data" format="saf" label="Input Signal" help="see below for more information on file format"/> + </when> <when value="CN"> - + <param name="input_cond" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/> <param name="nbcall" type="select" label="Number of calling classes" help="The number of levels to be used for calling. Either 3 (loss, normal, gain), 4 (including amplifications), 5 (including double deletions) "> <option value="3">3</option> <option value="4">4</option> @@ -50,7 +47,12 @@ </param> <param name="cellularity" type="float" size="5" value="1" min="0" max="1" label="Cellularity" help="Ratio of tumor cells in the sample. Real value between 0 and 1"/> </when> - </conditional> +</conditional> + + <param name="method" type="select" label="Segmentation method" help=""> + <option value="cghseg">cghseg</option> + <option value="PELT">PELT</option> + </param> <param name="outputgraph" type="select" label="Output figures"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> @@ -61,11 +63,16 @@ </param> </inputs> <outputs> - <data format="scr" name="output" label="segmentation of ${input.name}" /> - <data format="log" name="log" label="log of segmentation of ${input.name}"> + <data format="scr" name="outputC" label="segmentation of ${input.input_cond.name}" > + <filter>input['signal']=='CN'</filter> + </data> + <data format="sar" name="outputF" label="segmentation of ${input.input_cond.name}" > + <filter>input['signal']=='fracB'</filter> + </data> + <data format="log" name="log" label="log of segmentation of ${input.input_cond.name}"> <filter>outputlog == "TRUE"</filter> </data> - <data format="zip" name="graph" label="graph of segmentation of ${input.name}"> + <data format="zip" name="graph" label="graph of segmentation of ${input.input_cond.name}"> <filter>outputgraph == "TRUE"</filter> </data> </outputs>
--- a/selectionExtracted.xml Mon Apr 12 14:47:09 2021 +0000 +++ b/selectionExtracted.xml Tue Apr 20 13:11:24 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="markersSelection" name="Markers selection" version="1.2.0"> +<tool id="markersSelection" name="Markers selection" version="1.3.0"> <requirements> <container type="docker">sblanck/mpagenomicsdependencies</container> </requirements> @@ -26,10 +26,10 @@ <option value="logistic">Logistic</option> </param> - <param name="outputgraph" type="select" label="Output figures"> + <!--param name="outputgraph" type="select" label="Output figures"> <option value="TRUE">Yes</option> <option value="FALSE">No</option> - </param> + </param--> <param name="outputlog" type="select" label="Output log"> <option value="TRUE">Yes</option> <option value="FALSE">No</option>