Mercurial > repos > sblanck > mpagenomics
diff segmentation.xml @ 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 |
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--- 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>