Provided by: ctdconverter_2.1-6_all bug

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

       Copyright 2017, WorklfowConversion

       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.