diff tools/mira4_0/mira4_de_novo.xml @ 4:1713289d9908 draft default tip

v0.0.11 tweak for use with bioconda dependencies

--- a/tools/mira4_0/mira4_de_novo.xml	Fri Oct 02 06:12:23 2015 -0400
+++ b/tools/mira4_0/mira4_de_novo.xml	Thu Aug 10 11:09:10 2017 -0400
@@ -1,29 +1,24 @@
-<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.9">
+<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.11">
     <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
-        <requirement type="binary">mira</requirement>
-        <requirement type="binary">miraconvert</requirement>
         <requirement type="package" version="4.0.2">MIRA</requirement>
-        <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <code file="mira4_validator.py" />
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">mira4.py --version</version_command>
-    <command interpreter="python">mira4.py
---manifest "$manifest"
+    <version_command>
+python $__tool_directory__/mira4.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/mira4.py
+--manifest '$manifest'
 #if str($maf_wanted)=="true":
---maf "$out_maf"
+--maf '$out_maf'
 #end if
 #if str($bam_wanted)=="true":
---bam "$out_bam"
+--bam '$out_bam'
 #end if
---fasta "$out_fasta"
---log "$out_log"
+--fasta '$out_fasta'
+--log '$out_log'
     </command>
     <configfiles>
         <configfile name="manifest">
@@ -133,11 +128,11 @@
                 </when>
                 <when value="none" /><!-- no further questions -->
             </conditional>
-            <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
+            <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)"
                   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
         </repeat>
-        <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format?" checked="False" />
-        <param name="bam_wanted" type="boolean" label="Convert assembly into BAM format?" checked="True" />
+        <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format?" checked="false" />
+        <param name="bam_wanted" type="boolean" label="Convert assembly into BAM format?" checked="true" />
     </inputs>
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />