changeset 1:57d5928f456e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457

--- a/shovill.xml	Wed Oct 25 03:39:03 2017 -0400
+++ b/shovill.xml	Wed Mar 07 02:10:01 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="shovill" name="Shovill" version="0.8.0">
+<tool id="shovill" name="Shovill" version="0.9.0">
     <description>Faster SPAdes assembly of Illumina reads</description>
     <requirements>
-        <requirement type="package" version="0.8.0">shovill</requirement>
+        <requirement type="package" version="0.9.0">shovill</requirement>
     </requirements>
     <version_command>shovill --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -32,7 +32,7 @@
             --minlen $adv.minlen
             --mincov $adv.mincov
             --asm $adv.asm
-            
+
     ]]></command>
     <inputs>
         <conditional name="library">
@@ -45,7 +45,7 @@
                 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
             </when>
             <when value="collection">
-                <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> 
+                <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
         </conditional>
         <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
@@ -70,7 +70,7 @@
             </param>
         </section>
     </inputs>
-    
+
     <outputs>
         <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" >
             <filter>log</filter>
@@ -78,7 +78,7 @@
         <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
         <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/>
     </outputs>
-    
+
     <tests>
         <test> <!-- Test 0: Basic test -->
             <param name="lib_type" value="paired" />
@@ -122,7 +122,7 @@
                 <assert_contents>
                     <has_text text="Running: seqtk"/>
                     <has_text text="Running: kmc"/>
-                    <has_text text="Running: trimmomatic"/>
+                    <has_text_matching expression="Running:\s+\S+\s+trimmomatic"/>
                     <has_text text="Running: lighter"/>
                     <has_text text="Running: flash"/>
                     <has_text text="Running: spades"/>
@@ -142,8 +142,8 @@
     - Takes paired end Illumina fastq reads
     - Trim reads:   Use Trimmomatic to remove common adaptors first (default: OFF)
     - Output log file:  If set to "Yes", tool will return Shovill's log file as part of the output
-    
-Advanced options:    
+
+Advanced options:
     - Name format:          Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')
     - Depth:                Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)
     - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '')