Mercurial > repos > sblanck > mpagenomics
diff filter.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 |
line wrap: on
line diff
--- 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>