Mercurial > repos > peterjc > mira_assembler

changeset 11:e59904c855ae draft

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Uploaded v0.0.10, adds a test and updated download URL
author peterjc
date Wed, 30 Apr 2014 07:21:57 -0400
parents a2fb1e67bd11
children 63ebe9726219
files test-data/empty_file.dat tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/tool_dependencies.xml
diffstat 3 files changed, 70 insertions(+), 66 deletions(-) [+]
line wrap: on
line diff
--- a/tools/mira3/README.rst	Thu Jan 30 13:21:21 2014 -0500
+++ b/tools/mira3/README.rst	Wed Apr 30 07:21:57 2014 -0400
@@ -17,7 +17,7 @@
 ======================
 
 This should be straightforward, Galaxy should automatically download and
-install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
+install the precompiled binary for MIRA v3.4.1.1 for the Galaxy wrapper,
 and run any tests.
 
 
@@ -26,12 +26,12 @@
 
 There are just two Galaxy files to install:
 
-* mira.py (the Python script)
-* mira.xml (the Galaxy tool definition)
+* ``mira.py`` (the Python script)
+* ``mira.xml`` (the Galaxy tool definition)
 
-The suggested location is a new tools/mira3 folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
-this to tools_conf.xml.sample in order to run any tests::
+The suggested location is a new ``tools/mira3`` folder. You will also need to
+modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
+this to ``tools_conf.xml.sample`` in order to run any tests::
 
   <tool file="mira3/mira.xml" />
 
@@ -74,7 +74,9 @@
         - Updated citation information (Cock et al. 2013).
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
 v0.0.9  - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
-        - Correct path issue in automated dependency installation
+        - Correct path issue in automated dependency installation.
+v0.0.10 - Added a functional test.
+        - Updated URL for automated installation of MIRA v3.4.1.1
 ======= ======================================================================
 
 
@@ -90,7 +92,7 @@
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder::
 
-    $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
+    $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat
 
 Check this worked::
 
@@ -101,6 +103,7 @@
     tools/mira3/tool_dependencies.xml
     test-data/tvc_mini.fastq
     test-data/tvc_contigs.fasta
+    test-data/empty_file.dat
 
 
 Licence (MIT)
--- a/tools/mira3/mira.xml	Thu Jan 30 13:21:21 2014 -0500
+++ b/tools/mira3/mira.xml	Wed Apr 30 07:21:57 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
+<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.10">
     <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -72,61 +72,61 @@
         </param>
         <!-- Backbone -->
         <conditional name="condBackbone">
-           <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
-              <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
-           </when>
+            <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
+                <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
+            </when>
         </conditional>
         <!-- Sanger -->
         <conditional name="condSanger">
-           <param name="use" type="select" label="Sanger/Capillary reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="Sanger/Capillary reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
+            </when>
         </conditional>
         <!-- Roche 454 -->
         <conditional name="condRoche">
-           <param name="use" type="select" label="454 reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
-              <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="454 reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
+                <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
+            </when>
         </conditional>
         <!-- Illumina -->
         <conditional name="condIllumina">
-           <param name="use" type="select" label="Solexa/Illumina reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="Solexa/Illumina reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
+            </when>
         </conditional>
         <!-- Ion Torrent -->
         <conditional name="condIonTorrent">
-           <param name="use" type="select" label="Ion Torrent reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
-              <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
-           </when>
+            <param name="use" type="select" label="Ion Torrent reads?">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="false" />
+            <when value="true">
+                <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
+                <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
+            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -138,24 +138,25 @@
         <data name="out_log" format="txt" label="MIRA log" />
     </outputs>
     <tests>
-            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
-                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
-<!--
-Commenting out test until Galaxy framework is fixed,
-https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
+        <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
+             strain data and miraSearchESTSNPs. Here we just assemble it. --> 
         <test>
             <param name="job_method" value="denovo" />
             <param name="job_type" value="est" />
             <param name="job_qual" value="accurate" />
-            <param name="condBackbone.use" value="false" />
-            <param name="condSanger.use" value="true" />
-            <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
-            <param name="condRoche.use" value="false" />
-            <param name="condIllumina.use" value="false" /> 
-            <param name="condIonTorrent.use" value="false" />
+            <param name="condBackbone|use" value="false" />
+            <param name="condSanger|use" value="true" />
+            <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
+            <param name="condRoche|use" value="false" />
+            <param name="condIllumina|use" value="false" /> 
+            <param name="condIonTorrent|use" value="false" />
             <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
-	</test>
--->
+            <output name="out_qual" file="empty_file.dat" compare="contains" />
+            <output name="out_caf" file="empty_file.dat" compare="contains" />
+            <output name="out_ace" file="empty_file.dat" compare="contains" />
+            <output name="out_wig" file="empty_file.dat" compare="contains" />
+            <output name="out_log" file="empty_file.dat" compare="contains" />
+        </test>
     </tests>
     <help>
 
--- a/tools/mira3/tool_dependencies.xml	Thu Jan 30 13:21:21 2014 -0500
+++ b/tools/mira3/tool_dependencies.xml	Wed Apr 30 07:21:57 2014 -0400
@@ -4,7 +4,7 @@
         <install version="1.0">
             <actions>
                 <!-- Sourceforge doesn't offer nice clean download URLs which is a shame -->      
-                <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2</action>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/Older%20releases/V3.4.0/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2</action>
                 <action type="move_directory_files">
                     <source_directory>bin</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>