Mercurial > repos > sblanck > mpagenomics

diff extractCN.xml @ 5:4f753bb8681e draft

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"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/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>