Ubuntu Manpage: CTDConverter - Convert CTD files into Galaxy tool and CWL CommandLineTool files

NAME

       CTDConverter - Convert CTD files into Galaxy tool and CWL CommandLineTool files

DESCRIPTION

       CTDConverter        -        A        project        from       the       WorkflowConversion       family
       (https://github.com/WorkflowConversion/CTDConverter)

COPYRIGHT

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in
compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is
distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.

USAGE:

$ convert.py [FORMAT] [ARGUMENTS ...]

FORMAT can be either one of the supported output formats: cwl, galaxy.

There is one converter for each supported FORMAT, each taking a different set of arguments. Please
consult the detailed documentation for each of the converters. Nevertheless, all converters have the
following common parameters/options:

I - Parsing a single CTD file and convert it:

$ convert.py [FORMAT] -i [INPUT_FILE] -o [OUTPUT_FILE]

II - Parsing several CTD files, output converted wrappers in a given folder:

$ convert.py [FORMAT] -i [INPUT_FILES] -o [OUTPUT_DIRECTORY]

III - Hardcoding parameters

It is possible to hardcode parameters. This makes sense if you want to set a tool in 'quiet' mode
or if your tools support multi-threading and accept the number of threads via a parameter, without
giving end users the chance to change the values for these parameters.

In order to generate hardcoded parameters, you need to provide a simple file. Each line of this
file contains two or three columns separated by whitespace. Any line starting with a '#' will be
ignored. The first column contains the name of the parameter, the second column contains the value
that will always be set for this parameter. Only the first two columns are mandatory.

If the parameter is to be hardcoded only for a set of tools, then a third column can be added.
This column contains a comma-separated list of tool names for which the parameter will be
hardcoded. If a third column is not present, then all processed tools containing the given
parameter will get a hardcoded value for it.

The following is an example of a valid file:

##################################### HARDCODED PARAMETERS example
##################################### # Every line starting with a # will be handled as a comment
and will not be parsed. # The first column is the name of the parameter and the second column is
the value that will be used.

# Parameter name
# Value # Tool(s)

threads
8

mode quiet

xtandem_executable
xtandem XTandemAdapter

verbosity
high Foo, Bar

#########################################################################################################

Using the above file will produce a command-line similar to:

[TOOL] ... -threads 8 -mode quiet ...

for all tools. For XTandemAdapter, however, the command-line will look like:

XtandemAdapter ... -threads 8 -mode quiet -xtandem_executable xtandem ...

And for tools Foo and Bar, the command-line will be similar to:

Foo -threads 8 -mode quiet -verbosity high ...

IV - Engine-specific parameters

i - Galaxy

a. Providing file formats, mimetypes

Galaxy supports the concept of file format in order to connect compatible ports, that is, input
ports of a certain data format will be able to receive data from a port from the same format. This
converter allows you to provide a personalized file in which you can relate the CTD data formats
with supported Galaxy data formats. The layout of this file consists of lines, each of either one
or four columns separated by any amount of whitespace. The content of each column is as follows:

* 1st column: file extension * 2nd column: data type, as listed in Galaxy * 3rd column: full-named
Galaxy data type, as it will appear on datatypes_conf.xml * 4th column: mimetype (optional)

The following is an example of a valid "file formats" file:

########################################## FILE FORMATS example
########################################## # Every line starting with a # will be handled as a
comment and will not be parsed. # The first column is the file format as given in the CTD and
second column is the Galaxy data format. The # second, third, fourth and fifth columns can be left
empty if the data type has already been registered # in Galaxy, otherwise, all but the mimetype
must be provided.

# CTD type
# Galaxy type # Long Galaxy data type # Mimetype

csv tabular galaxy.datatypes.data:Text

fasta ini txt galaxy.datatypes.data:Text txt idxml txt
galaxy.datatypes.xml:GenericXml application/xml options txt
galaxy.datatypes.data:Text grid grid galaxy.datatypes.data:Grid
##########################################################################################################

Note that each line consists precisely of either one, three or four columns. In the case of data
types already registered in Galaxy (such as fasta and txt in the above example), only the first
column is needed. In the case of data types that haven't been yet registered in Galaxy, the first
three columns are needed (mimetype is optional).

For information about Galaxy data types and subclasses, see the following page:
https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes

b. Finer control over which tools will be converted

Sometimes only a subset of CTDs needs to be converted. It is possible to either explicitly specify
which tools will be converted or which tools will not be converted.

The value of the -s/--skip-tools parameter is a file in which each line will be interpreted as the
name of a tool that will not be converted. Conversely, the value of the -r/--required-tools is a
file in which each line will be interpreted as a tool that is required. Only one of these
parameters can be specified at a given time.

The format of both files is exactly the same. As stated before, each line will be interpreted as
the name of a tool. Any line starting with a '#' will be ignored.

ii - CWL

There are, for now, no CWL-specific parameters or options.

python3 convert.py 2.1 July 2023 CTDCONVERTER(1)