Mercurial > repos > gga > tripal_analysis_load_fasta
changeset 1:43bb9308b52d draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
| author | gga |
|---|---|
| date | Tue, 19 Sep 2017 12:24:58 -0400 |
| parents | ca1eb54c95d6 |
| children | 0fbe72b81b9e |
| files | README.rst analysis_load_fasta.xml |
| diffstat | 2 files changed, 50 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Sep 19 12:24:58 2017 -0400 @@ -0,0 +1,46 @@ +Galaxy-tripal +============= + +Galaxy tools to interface with Tripal using pyhon-tripal + +Dependencies +------------ + +You will need to install some python modules in the Galaxy virtualenv for these +tools to be fully functional: + +.. code:: bash + + . /path/to/galaxy/.venv/bin/activate + pip install future tripal + deactivate + +Environment +----------- + +The following environment variables must be set: + ++--------------------------------+-----------------------------------------------------------+ +| ENV | Use | ++================================+===========================================================+ +| ``$GALAXY_TRIPAL_URL`` | The URL at which Tripal is accessible, internal to Galaxy | +| | and where the tools run. Must be absolute, with FQDN and | +| | protocol. | ++--------------------------------+-----------------------------------------------------------+ +| ``$GALAXY_TRIPAL_USER`` | The admin user which Galaxy should use to talk to Tripal. | +| | | ++--------------------------------+-----------------------------------------------------------+ +| ``$GALAXY_TRIPAL_PASSWORD`` | The password for the admin user. | +| | | +| | | ++--------------------------------+-----------------------------------------------------------+ +| ``$GALAXY_TRIPAL_SHARED_DIR`` | Directory shared between Galaxy and Tripal, used to | +| | exchange data files. | ++--------------------------------+-----------------------------------------------------------+ + + +License +------- + +All python scripts, wrappers, and the webapollo.py are licensed under +MIT license.
--- a/analysis_load_fasta.xml Mon Sep 11 05:50:45 2017 -0400 +++ b/analysis_load_fasta.xml Tue Sep 19 12:24:58 2017 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="analysis_load_fasta" profile="16.04" name="Load a Fasta file" version="@WRAPPER_VERSION@.0"> +<tool id="analysis_load_fasta" profile="16.04" name="Load a Fasta file" version="@WRAPPER_VERSION@.1"> <description>into Tripal</description> <macros> <import>macros.xml</import> @@ -28,7 +28,9 @@ --method '${loading.method}' - --match_type '${loading.match_type}' + #if str($loading.method) != "insert": + --match_type '${loading.match_type}' + #end if #if str($naming.re_name): --re_name '${naming.re_name}'