diff tools/mira4_0/mira4_bait.xml @ 4:1713289d9908 draft default tip

v0.0.11 tweak for use with bioconda dependencies

--- a/tools/mira4_0/mira4_bait.xml	Fri Oct 02 06:12:23 2015 -0400
+++ b/tools/mira4_0/mira4_bait.xml	Thu Aug 10 11:09:10 2017 -0400
@@ -1,21 +1,17 @@
-<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.9">
+<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.11">
     <description>Filter reads using kmer matches</description>
     <requirements>
-        <requirement type="binary">mirabait</requirement>
         <requirement type="package" version="4.0.2">MIRA</requirement>
     </requirements>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">mira4_bait.py --version</version_command>
-    <command interpreter="python">
-mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence "$bait_file" "$input_reads" "$output_reads"
+    <version_command>
+python $__tool_directory__/mira4_bait.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence '$bait_file' '$input_reads' '$output_reads'
     </command>
     <inputs>
-        <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
-        <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
+        <param name="bait_file" type="data" format="fasta,fastq,mira" label="Bait file (what to look for)" />
+        <param name="input_reads" type="data" format="fasta,fastq,mira" label="Reads to search" />
         <param name="output_choice" type="select" label="Output positive matches, or negative matches?">
             <option value="pos">Just positive matches</option>
             <option value="neg">Just negative matches</option>
@@ -32,7 +28,7 @@
     </inputs>
     <outputs>
         <data name="output_reads" format_source="input_reads" metadata_source="input_reads"
-	      label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/>
+              label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/>
     </outputs>
     <tests>
         <test>