# HG changeset patch
# User peterjc
# Date 1495129002 14400
# Node ID b20e9df573175bfd44078cfe41c4bee258fed9d9
# Parent  e9b376c61f03873c1b1cbccba4a565c604887609
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit fd979d17340cde155de176604744831d9597c6b6

diff -r e9b376c61f03 -r b20e9df57317 tools/mira4_9/README.rst
--- a/tools/mira4_9/README.rst	Wed Feb 10 09:07:48 2016 -0500
+++ b/tools/mira4_9/README.rst	Thu May 18 13:36:42 2017 -0400
@@ -11,9 +11,6 @@
 It is available from the Galaxy Tool Shed at:
 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_9
 
-Development/test previews are available from the Galaxy Test Tool Shed at:
-http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_9
-
 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format,
 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
 
@@ -27,7 +24,7 @@
 ======================
 
 This should be straightforward. Via the Tool Shed, Galaxy should automatically
-install the ``mira`` datatype, samtools, and download and install the precompiled
+install the `mira` datatype, samtools, and download and install the precompiled
 binary for MIRA v4.9.5 for the Galaxy wrapper, and offer to run any tests.
 
 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
diff -r e9b376c61f03 -r b20e9df57317 tools/mira4_9/mira_4_9_bait.xml
--- a/tools/mira4_9/mira_4_9_bait.xml	Wed Feb 10 09:07:48 2016 -0500
+++ b/tools/mira4_9/mira_4_9_bait.xml	Thu May 18 13:36:42 2017 -0400
@@ -1,19 +1,16 @@
 <tool id="mira_4_9_bait" name="MIRA v4.9 mirabait" version="0.0.1">
     <description>Filter reads using kmer matches</description>
     <requirements>
-        <requirement type="binary">mirabait</requirement>
         <requirement type="package" version="4.9.5">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">mira_check_version.py ${MIRA4_9}mirabait</version_command>
-    <command interpreter="python">./mira_check_version.py \${MIRA4_9}mirabait 4.9 &amp;&amp;
+    <version_command>
+python $__tool_directory__/mira_check_version.py ${MIRA4_9}mirabait
+    </version_command>
+    <command detect_errors="aggressive" strict="true">
+python $__tool_directory__/mira_check_version.py \${MIRA4_9}mirabait 4.9 &amp;&amp;
 ##First checked it is mirabait v4.9 on the path... now actually run it
 ##-----------------------------------------------------------------------
-\${MIRA4_9}mirabait -k "$kmer_length" -n "$min_occurence" -b "$bait_file"
+\${MIRA4_9}mirabait -k '$kmer_length' -n '$min_occurence' -b '$bait_file'
 ##-----------------------------------------------------------------------
 ##Must now map Galaxy datatypes to MIRA file types...
 ##exploiting the polymorphic naming of the input read parameter!
@@ -25,15 +22,15 @@
  -f maf -t maf
 #else
 ##MIRA is happy with fasta as name,
- -f "$reads.filename.ext" -t "$reads.filename.ext"
+ -f '$reads.filename.ext' -t '$reads.filename.ext'
 #end if
 ##-----------------------------------------------------------------------
 #if str($output_choice_cond.output_choice)=="both"
--o "$output_pos" -O "$output_neg"
+-o '$output_pos' -O '$output_neg'
 #elif str($output_choice_cond.output_choice)=="pos"
--o "$output_pos"
+-o '$output_pos'
 #elif str($output_choice_cond.output_choice)=="neg"
--i -O "$output_neg"
+-i -O '$output_neg'
 #end if
 ##-----------------------------------------------------------------------
 ##Do we need to ignore the reverse strand?
@@ -51,17 +48,17 @@
 ##TODO: Is there a better way to signal an error to Galaxy here?
 ; echo "ERROR: Paired read datatype mis-match!" ; false
 #end if
--p "$reads.filename" "$reads.filename2"
+-p '$reads.filename' '$reads.filename2'
 #elif str($reads.type) == "interleaved"
--P "$reads.filename"
+-P '$reads.filename'
 #elif str($reads.type) == "none"
-"$reads.filename"
+'$reads.filename'
 #end if
     </command>
     <inputs>
         <!-- TODO: mirabait now allows multiple input files, and can do multiple outputs - or merge into one? -->
         <!-- TODO: define a new Galaxy datatype for the bait hash file? -->
-        <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
+        <param name="bait_file" type="data" format="fasta,fastq,mira" label="Bait file (what to look for)" />
         <conditional name="reads">
             <param name="type" type="select" label="Are these paired reads?">
                 <option value="paired">Paired reads (as two files)</option>
@@ -69,14 +66,14 @@
                 <option value="none">Unpaired reads (single or orphan reads as one file)</option>
             </param>
             <when value="paired">
-                <param name="filename" type="data" format="fastq,fasta" required="true" label="Read file one"/>
-                <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/>
+                <param name="filename" type="data" format="fastq,fasta" label="Read file one"/>
+                <param name="filename2" type="data" format="fastq,fasta" label="Read file two"/>
             </when>
             <when value="interleaved">
-                <param name="filename" type="data" format="fasta,fastq" required="true" label="Interleaved paired reads to search" />
+                <param name="filename" type="data" format="fasta,fastq" label="Interleaved paired reads to search" />
             </when>
             <when value="none">
-                <param name="filename" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
+                <param name="filename" type="data" format="fasta,fastq,mira" label="Reads to search" />
             </when>
         </conditional>
         <conditional name="output_choice_cond">
diff -r e9b376c61f03 -r b20e9df57317 tools/mira4_9/repository_dependencies.xml
--- a/tools/mira4_9/repository_dependencies.xml	Wed Feb 10 09:07:48 2016 -0500
+++ b/tools/mira4_9/repository_dependencies.xml	Thu May 18 13:36:42 2017 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format).">
-    <repository changeset_revision="54318d4bcadd" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="94e05a9e3957" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r e9b376c61f03 -r b20e9df57317 tools/mira4_9/tool_dependencies.xml
--- a/tools/mira4_9/tool_dependencies.xml	Wed Feb 10 09:07:48 2016 -0500
+++ b/tools/mira4_9/tool_dependencies.xml	Thu May 18 13:36:42 2017 -0400
@@ -4,6 +4,6 @@
         <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="MIRA" version="4.9.5">
-        <repository changeset_revision="645a9fb69d42" name="package_mira_4_9_5" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="28020b797d22" name="package_mira_4_9_5" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>