Mercurial > repos > peterjc > mira_assembler
changeset 11:e59904c855ae draft
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(-) [+] |
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--- 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>