diff ectyper.xml @ 22:6633619837ad draft default tip

planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty

--- a/ectyper.xml	Wed Jan 10 13:39:06 2018 -0500
+++ b/ectyper.xml	Mon Mar 12 09:52:17 2018 -0400
@@ -1,28 +1,44 @@
 <tool id="ectyper" name="ectyper" version="0.1">
     <requirements>
       <requirement type="package" version="0.1">ectyper</requirement>
+      <requirement type="package" version="3.5">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if $jobtype.select == "asm"
-        ln -s $jobtype.draft sample.fasta;  
+        ln -s $jobtype.draft ${draft.name}.fasta;  
       #else if $jobtype.select == "se"
-        ln -s $jobtype.fastq1 sample_1.fastq;  
+        ln -s $jobtype.fastq1 ${fastq1.name}_1.fastq;  
       #else if $jobtype.select == "pe"
-        ln -s $jobtype.fastq1 sample_1.fastq;  
-        ln -s $jobtype.fastq2 sample_2.fastq;  
+        ln -s $jobtype.fastq1 ${fastq1.name}.fastq;  
+        ln -s $jobtype.fastq2 ${fastq2.name}.fastq;  
+      #else if $jobtype.select == "cl"
+        mkdir temp_data;
+        #for $collection_file in $jobtype.collection_files
+             cp $collection_file temp_data/.;
+        #end for
+
+      $__tool_directory__/ectyper  -i temp_data 
+      -d $percent_identity
+	    -l $percent_length
+  	  -o "./"; cat ./output/output.csv > results.csv; 
+
+      GALAXY_URL
       #end if
 
-	  $__tool_directory__/ectyper 
+
+    #if $jobtype.select != "cl"
+    	$__tool_directory__/ectyper 
       #if $jobtype.select == "asm"
-        -i sample.fasta
+        -i ${draft.name}.fasta
       #else if $jobtype.select == "se"
-        -i sample_1.fastq
+        -i ${fastq1.name}_1.fastq
       #else if $jobtype.select == "pe"
-        -i sample_1.fastq sample_2.fastq
+        -i ${fastq1.name}.fastq,${fastq2.name}.fastq
       #end if
       -d $percent_identity
 	  -l $percent_length
-  	  -o "./"; cat ./output/output.csv > results.csv; 
+  	  -o "./"; cat ./output/output.csv > results.csv;
+    #end if 
 
     ]]></command>
     <inputs>
@@ -31,6 +47,7 @@
           <option value="asm">Genome Assembly</option>
           <option value="se">Single-End Reads</option>
           <option value="pe">Paired-End Reads</option>
+          <option value="cl">Collection of Reads</option>
         </param>
         <when value="asm">
           <param name="draft" type="data" format="fasta" label="FASTA" />
@@ -42,8 +59,11 @@
           <param name="fastq1" type="data" format="fastq" label="FASTQ" />
           <param name="fastq2" type="data" format="fastq" label="FASTQ" />
         </when>
+         <when value="cl">
+              <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
+        </when>
       </conditional>
-
+   
       <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
       <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
     
@@ -58,7 +78,7 @@
 
 **INPUT**
 
-A fasta assembly or single or paired end reads
+A fasta assembly or single or paired end reads test or data set list of fastqs
 
 **PERCENTIDENTITY**
 
@@ -71,4 +91,4 @@
 https://github.com/phac-nml/ecoli_serotyping
 
     ]]></help>
-</tool>
+</tool>
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