WorkflowConversion / CTDConverter

Series of python scripts to convert CTD files into other formats such as Galaxy, CWL
MIT License
5 stars 8 forks source link

CWL: \n is not valid YAML, nor do URLs need wrapping in <> #37

Open mr-c opened 6 years ago

mr-c commented 6 years ago

From lamda --write-ctd

<?xml version="1.0" encoding="UTF-8"?>
<tool name="Lambda" version="1.0.2 (Git commit )" docurl="http://www.seqan.de" category="" >
        <executableName>lambda</executableName>
        <description>the Local Aligner for Massive Biological DatA</description>
        <manual>Lambda is a local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.
Detailed information is available in the wiki: &lt;https://github.com/seqan/lambda/wiki&gt;
</manual>

produces via convert.py cwl

#!/usr/bin/env cwl-runner

# This CWL file was automatically generated using CTDConverter.
# Visit https://github.com/WorkflowConversion/CTDConverter for more information.

baseCommand: lambda
class: CommandLineTool
cwlVersion: v1.0
doc: "Lambda is a local aligner optimized for many query sequences and searches in\
  \ protein space. It is compatible to BLAST, but much faster than BLAST and many\
  \ other comparable tools.\nDetailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>\n\
  \n\n\nFor more information, visit http://www.seqan.de"

which could be as

#!/usr/bin/env cwl-runner

# This CWL file was automatically generated using CTDConverter.
# Visit https://github.com/WorkflowConversion/CTDConverter for more information.

baseCommand: lambda
class: CommandLineTool
cwlVersion: v1.0
doc: |
  Lambda is a local aligner optimized for many query sequences and searches in
  protein space. It is compatible to BLAST, but much faster than BLAST and many
  other comparable tools.
  Detailed information is available in the wiki: https://github.com/seqan/lambda/wiki

  For more information, visit http://www.seqan.de