| Previous changeset 6:0f6eb4a75000 (2015-08-05) Next changeset 8:60a9b3f760cc (2017-02-01) |
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Commit message:
v0.0.16, adding new model TTSS-STD-2.0.2.jar |
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modified:
tool-data/effectiveT3.loc.sample tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.xml tools/effectiveT3/tool_dependencies.xml |
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added:
test-data/four_human_proteins.effectiveT3_std2.tabular |
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| diff -r 0f6eb4a75000 -r 5f85301d50bf test-data/four_human_proteins.effectiveT3_std2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.effectiveT3_std2.tabular Mon Sep 21 05:52:29 2015 -0400 |
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| @@ -0,0 +1,5 @@ +#ID Description Score Effective +sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 1.000000000000000 true +sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 0.999238327753953 true +sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 0.000000000000345 false +sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 0.000000000000000 false |
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| diff -r 0f6eb4a75000 -r 5f85301d50bf tool-data/effectiveT3.loc.sample --- a/tool-data/effectiveT3.loc.sample Wed Aug 05 11:04:42 2015 -0400 +++ b/tool-data/effectiveT3.loc.sample Mon Sep 21 05:52:29 2015 -0400 |
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| @@ -14,6 +14,7 @@ #e.g. # # /opt/EffectiveT3/TTSS_GUI-1.0.1.jar +# /opt/EffectiveT3/module/TTSS_STD-2.0.2.jar # /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar # /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar # /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar @@ -21,6 +22,7 @@ #See files ../tools/protein_analysis/effectiveT3.* for more details, #and http://effectors.org # -standard Type III Effector prediction with standard set TTSS_STD-1.0.1.jar -animal Type III Effector prediction with animal set TTSS_ANIMAL-1.0.1.jar -plant Type III Effector prediction with plant set TTSS_PLANT-1.0.1.jar +std_2_0_2 Type III Effector prediction with standard set (v2.0.2, Sep 2015) TTSS_STD-2.0.2.jar +standard Type III Effector prediction with standard set (v1.0.1, Aug 2009) TTSS_STD-1.0.1.jar +animal Type III Effector prediction with human/animal-associated set (v1.0.1, Aug 2009) TTSS_ANIMAL-1.0.1.jar +plant Type III Effector prediction with plant-associated set (v1.0.1, Aug 2009) TTSS_PLANT-1.0.1.jar |
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| diff -r 0f6eb4a75000 -r 5f85301d50bf tools/effectiveT3/README.rst --- a/tools/effectiveT3/README.rst Wed Aug 05 11:04:42 2015 -0400 +++ b/tools/effectiveT3/README.rst Mon Sep 21 05:52:29 2015 -0400 |
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| @@ -27,7 +27,8 @@ ====================== This should be straightforward, Galaxy should automatically download and install -the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std). +the Jar files for effectiveT3 v1.0.1 and its associated models (animal, plant and +standard). Manual Installation @@ -73,7 +74,7 @@ Version Changes ------- ---------------------------------------------------------------------- v0.0.7 - Initial public release -v0.0.8 - Include effectiveT3.loc.sample in Tool Shed +v0.0.8 - Include ``effectiveT3.loc.sample`` in Tool Shed v0.0.9 - Check the return code for errors in the XML v0.0.10 - Added unit test v0.0.11 - Automated installation @@ -89,6 +90,10 @@ v0.0.14 - Fixed error handling in ``effectiveT3.py``. v0.0.15 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.0.16 - Updated URLs to download the tool and models. + - Includes new standard classification model v2.0.2 (Sep 2015) + as the default entry in ``tool-data/effectiveT3.loc`` + - Catch java exception, e.g. if Java too old for ``TTSS-STD-2.0.1.jar`` ======= ====================================================================== @@ -105,12 +110,12 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/ + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/ ... or:: - $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/ + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/ ... To just build and check the tar ball, use:: |
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| diff -r 0f6eb4a75000 -r 5f85301d50bf tools/effectiveT3/effectiveT3.py --- a/tools/effectiveT3/effectiveT3.py Wed Aug 05 11:04:42 2015 -0400 +++ b/tools/effectiveT3/effectiveT3.py Mon Sep 21 05:52:29 2015 -0400 |
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| @@ -21,7 +21,7 @@ if "-v" in sys.argv or "--version" in sys.argv: # TODO - Get version of the JAR file dynamically? - print("Wrapper v0.0.14, TTSS_GUI-1.0.1.jar") + print("Wrapper v0.0.16, TTSS_GUI-1.0.1.jar") sys.exit(0) def sys_exit(msg, error_level=1): @@ -83,13 +83,14 @@ # Use .communicate as can get deadlocks with .wait(), stdout, stderr = child.communicate() return_code = child.returncode - if return_code: + if return_code or stderr.startswith("Exception in thread"): cmd_str= " ".join(cmd) # doesn't quote spaces etc if stderr and stdout: sys_exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) else: sys_exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) + if not os.path.isdir(effectiveT3_dir): sys_exit("Effective T3 folder not found: %r" % effectiveT3_dir) |
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| diff -r 0f6eb4a75000 -r 5f85301d50bf tools/effectiveT3/effectiveT3.xml --- a/tools/effectiveT3/effectiveT3.xml Wed Aug 05 11:04:42 2015 -0400 +++ b/tools/effectiveT3/effectiveT3.xml Mon Sep 21 05:52:29 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="effectiveT3" name="Effective T3" version="0.0.15"> +<tool id="effectiveT3" name="Effective T3" version="0.0.16"> <description>Find bacterial effectors in protein sequences</description> <requirements> <requirement type="package" version="1.0.1">effectiveT3</requirement> @@ -50,6 +50,13 @@ <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" lines_diff="2"/> </test> <test> + <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="module" value="std_2_0_2" /> + <param name="type" value="cutoff" /> + <param name="cutoff" value="0.8" /> + <output name="tabular_file" file="four_human_proteins.effectiveT3_std2.tabular" ftype="tabular" /> + </test> + <test> <param name="fasta_file" value="empty.fasta" ftype="fasta" /> <param name="module" value="plant" /> <param name="type" value="sensitive" /> |
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| diff -r 0f6eb4a75000 -r 5f85301d50bf tools/effectiveT3/tool_dependencies.xml --- a/tools/effectiveT3/tool_dependencies.xml Wed Aug 05 11:04:42 2015 -0400 +++ b/tools/effectiveT3/tool_dependencies.xml Mon Sep 21 05:52:29 2015 -0400 |
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| @@ -8,22 +8,24 @@ <environment_variable name="EFFECTIVET3" action="set_to">$INSTALL_DIR</environment_variable> </action> <!-- Main JAR file --> - <action type="shell_command">wget http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> + <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_GUI-1.0.1.jar</action> <!-- If using action type download_file will need to move the file, <action type="move_file"><source>TTSS_GUI-1.0.1.jar</source><destination>$INSTALL_DIR/</destination></action> --> <!-- Three model JAR files --> <action type="make_directory">$INSTALL_DIR/module</action> - <action type="shell_command">wget http://effectors.org/download/module/TTSS_ANIMAL-1.0.1.jar</action> + <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_ANIMAL-1.0.1.jar</action> <action type="move_file"><source>TTSS_ANIMAL-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action> - <action type="shell_command">wget http://effectors.org/download/module/TTSS_PLANT-1.0.1.jar</action> + <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_PLANT-1.0.1.jar</action> <action type="move_file"><source>TTSS_PLANT-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action> - <action type="shell_command">wget http://effectors.org/download/module/TTSS_STD-1.0.1.jar</action> + <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-1.0.1.jar</action> <action type="move_file"><source>TTSS_STD-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action> + <action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-2.0.2.jar</action> + <action type="move_file"><source>TTSS_STD-2.0.2.jar</source><destination>$INSTALL_DIR/module/</destination></action> </actions> </install> <readme> -Downloads effectiveT3 v1.0.1 and the three models from http://effectors.org/ +Downloads effectiveT3 v1.0.1 and associated models from http://effectors.org/ aka http://effectors.csb.univie.ac.at/ </readme> </package> </tool_dependency> |