# HG changeset patch
# User peterjc
# Date 1392890839 18000
# Node ID b0ffe0e7282b2e8c088d6cfe4af4da6cfe438e89
# Parent  133b863a8a403e18965b845967654c508bcdb71c
Uploaded v0.0.2 preview 7, fixed bash syntax error

diff -r 133b863a8a40 -r b0ffe0e7282b tools/mira4/mira4_bait.xml
--- a/tools/mira4/mira4_bait.xml	Mon Feb 17 06:12:41 2014 -0500
+++ b/tools/mira4/mira4_bait.xml	Thu Feb 20 05:07:19 2014 -0500
@@ -14,8 +14,8 @@
         <exit_code range=":-1" />
     </stdio>
     <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" 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="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>
@@ -24,11 +24,11 @@
             <option value="both">Check both strands</option>
             <option value="fwd">Just forward strand</option>
         </param>
-	<param name="kmer_length" type="integer" value="31" min="1" max="32"
-	       label="k-mer length" help="Maximum 32" />
-	<param name="min_occurence" type="integer" value="1" min="1"
-	       label="Minimum k-mer occurence"
-	       help="How many k-mer matches do you want per read? Minimum one" />
+        <param name="kmer_length" type="integer" value="31" min="1" max="32"
+               label="k-mer length" help="Maximum 32" />
+        <param name="min_occurence" type="integer" value="1" min="1"
+               label="Minimum k-mer occurence"
+               help="How many k-mer matches do you want per read? Minimum one" />
     </inputs>
     <outputs>
         <data name="output_reads" format="fasta" label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name">
@@ -40,7 +40,7 @@
                 <when input_dataset="input_reads" attribute="extension" value="fastqillumina" format="fastqillumina" />
                 <when input_dataset="input_reads" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
             </change_format>
-	</data>
+        </data>
     </outputs>
     <tests>
         <test>
diff -r 133b863a8a40 -r b0ffe0e7282b tools/mira4/mira4_de_novo.xml
--- a/tools/mira4/mira4_de_novo.xml	Mon Feb 17 06:12:41 2014 -0500
+++ b/tools/mira4/mira4_de_novo.xml	Thu Feb 20 05:07:19 2014 -0500
@@ -34,7 +34,7 @@
                 <option value="pcbiolq">PacBio low quality (raw)</option>
                 <option value="pcbiohq">PacBio high quality (corrected)</option>
                 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
-		<!-- TODO reference/backbone as an entry here? -->
+                <!-- TODO reference/backbone as an entry here? -->
             </param>
             <conditional name="segments">
                 <param name="type" type="select" label="Are these paired reads?">
@@ -64,8 +64,8 @@
                 </when>
                 <when value="none" /><!-- no further questions -->
             </conditional>
-	    <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" 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)." />
+            <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" 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>
     </inputs>
     <code file="mira4_validator.py" />
@@ -161,10 +161,10 @@
             <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
         </test>
         -->
-	<!-- Simple assembly based on MIRA's minidemo/solexa1 example
+    <!-- Simple assembly based on MIRA's minidemo/solexa1 example
              Note we're using just one repeat group,
              but two parameters within the repeat (filename, no pairing)
-	     -->
+         -->
         <test>
             <param name="job_type" value="genome" />
             <param name="job_quality" value="accurate" />
diff -r 133b863a8a40 -r b0ffe0e7282b tools/mira4/mira4_mapping.xml
--- a/tools/mira4/mira4_mapping.xml	Mon Feb 17 06:12:41 2014 -0500
+++ b/tools/mira4/mira4_mapping.xml	Thu Feb 20 05:07:19 2014 -0500
@@ -25,11 +25,11 @@
             <option value="accurate">Accurate</option>
             <option value="draft">Draft</option>
         </param>
-	<!-- TODO? Allow technology type for references? -->
-	<!-- TODO? Allow strain settings for reference(s) and reads? -->
-	<!-- TODO? Use a repeat to allow for multi-strain references? -->
+        <!-- TODO? Allow technology type for references? -->
+        <!-- TODO? Allow strain settings for reference(s) and reads? -->
+        <!-- TODO? Use a repeat to allow for multi-strain references? -->
         <!-- TODO? Add strain to the mapping read groups? -->
-	<param name="references" type="data" format="fasta,fastq,mira" multiple="true" required="true" label="Backbone reference file(s)"
+        <param name="references" type="data" format="fasta,fastq,mira" multiple="true" required="true" label="Backbone reference file(s)"
                help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." />
         <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)">
             <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option>
diff -r 133b863a8a40 -r b0ffe0e7282b tools/mira4/tool_dependencies.xml
--- a/tools/mira4/tool_dependencies.xml	Mon Feb 17 06:12:41 2014 -0500
+++ b/tools/mira4/tool_dependencies.xml	Thu Feb 20 05:07:19 2014 -0500
@@ -24,12 +24,12 @@
                 </actions>
                 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
                 <actions>
-                    <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action>
-                    <action type="shell_command">echo Your machine details (the output from 'uname' and 'arch'):</action>
+                    <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
+                    <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
                     <action type="shell_command">uname</action>
                     <action type="shell_command">arch</action>
-                    <action type="shell_command">echo If pre-compiled MIRA binaries are now available for this, please report this</action>
-                    <action type="shell_command">echo via https://github.com/peterjc/pico_galaxyt/issues - thank you!</action>
+                    <action type="shell_command">echo "If pre-compiled MIRA binaries are now available for this, please report this"</action>
+                    <action type="shell_command">echo "via https://github.com/peterjc/pico_galaxyt/issues - thank you!"</action>
                     <action type="shell_command">false</action>
                     <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
                 </actions>