diff dada2_plotQualityProfile.xml @ 5:863ebf0d28d5 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38

--- a/dada2_plotQualityProfile.xml	Mon Apr 29 09:49:29 2019 -0400
+++ b/dada2_plotQualityProfile.xml	Sun May 05 12:26:15 2019 -0400
@@ -6,25 +6,50 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-        Rscript --slave '$dada2_script'
+##name files by linking
+#import re
+#if "batch" in str($paired_cond.paired_select)
+  #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier))
+  #if "single" in str($paired_cond.paired_select)
+    ln -s '$paired_cond.fl' '$elid' &&
+  #else
+    ln -s '$paired_cond.fl.forward' '$elid'_forward &&
+    ln -s '$paired_cond.fl.reverse' '$elid'_reverse &&
+  #end if
+#else
+  #for $read in $paired_cond.fl:
+    #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
+    #if "single" in str($paired_cond.paired_select)
+      ln -s '$read' '$elid' &&
+    #else
+      ln -s '$read.forward' '$elid'_forward &&
+      ln -s '$read.reverse' '$elid'_reverse &&
+    #end if
+  #end for
+#end if
+	
+	Rscript --slave '$dada2_script'
     ]]></command>
     <configfiles>
         <configfile name="dada2_script"><![CDATA[
+#import re
 files = c()
 #if "batch" in str($paired_cond.paired_select)
+  #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier))
   #if "single" in str($paired_cond.paired_select)
-    files = c(files, '$paired_cond.reads')
+    files = c(files, '$elid')
   #else
-    files = c(files, '$paired_cond.reads.forward')
-    files = c(files, '$paired_cond.reads.reverse')
+    files = c(files, paste('$elid', 'forward', sep = "_"))
+    files = c(files, paste('$elid', 'reverse', sep = "_"))
   #end if
 #else
-  #for $read in $paired_cond.reads:
+  #for $read in $paired_cond.fl:
+    #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
     #if "single" in str($paired_cond.paired_select)
-      files = c(files, '$read')
+      files = c(files, '$elid')
     #else
-      files = c(files, '$read.forward')
-      files = c(files, '$read.reverse')
+      files = c(files, paste('$elid', 'forward', sep = "_"))
+      files = c(files, paste('$elid', 'reverse', sep = "_"))
     #end if
   #end for
 #end if
@@ -50,16 +75,16 @@
                 <option value="single_batch">single - batch</option>
             </param>
             <when value="paired">
-                <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
+                <param argument="fl" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
             </when>
             <when value="single">
-                <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
+                <param argument="fl" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
             </when>
             <when value="paired_batch">
-                <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
+                <param argument="fl" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
             </when>
             <when value="single_batch">
-                <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
+                <param argument="fl" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
             </when>
         </conditional>
         <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/>
@@ -73,7 +98,7 @@
         <test>
             <param name="aggregate" value="TRUE"/>
             <param name="paired_cond|paired_select" value="paired"/>
-            <param name="paired_cond|reads">
+            <param name="paired_cond|fl">
                 <collection type="list:paired">
                     <element name="F3D0_S188_L001">
                         <collection type="paired">
@@ -89,7 +114,7 @@
         <test>
             <param name="aggregate" value="FALSE"/>
             <param name="paired_cond|paired_select" value="paired_batch"/>
-            <param name="paired_cond|reads">
+            <param name="paired_cond|fl">
                 <collection type="paired">
                     <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
                     <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
@@ -101,7 +126,7 @@
         <test>
             <param name="aggregate" value="TRUE"/>
             <param name="paired_cond|paired_select" value="single"/>
-            <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="n" value="10000"/>
             <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
         </test>
@@ -109,7 +134,7 @@
         <test>
             <param name="aggregate" value="FALSE"/>
             <param name="paired_cond|paired_select" value="single_batch"/>
-            <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="n" value="10000"/>
             <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/>
         </test>    </tests>