planemo lint does not validate file formats

[peterjc]

e.g. Using format="foobar" could be caught as an error during linting:

$ planemo --version
planemo, version 0.41.0.dev0
$ git diff
diff --git a/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml b/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml
index 6bc8c54..34521e8 100644
--- a/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml
+++ b/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml
@@ -17,7 +17,7 @@ python $__tool_directory__/fastq_paired_unpaired.py '$input_fastq.extension' '$i
 $output_singles
     </command>
     <inputs>
-        <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
+        <param name="input_fastq" type="data" format="foobar" label="FASTQ file to divide into paired and unpaired reads"/>
         <conditional name="output_choice_cond">
             <param name="output_choice" type="select" label="How to output paired reads?">
                 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
$ planemo lint tools/fastq_paired_unpaired/fastq_paired_unpaired.xml ; echo "Return code $?"
Linting tool /mnt/shared/users/xxx/repositories/pico_galaxy/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml
Applying linter tests... CHECK
.. CHECK: 2 test(s) found.
Applying linter output... CHECK
.. INFO: 4 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 2 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.4].
.. CHECK: Tool defines a name [Divide FASTQ file into paired and unpaired reads].
.. CHECK: Tool defines an id [fastq_paired_unpaired].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... CHECK
.. CHECK: Found 1 likely valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Return code 0

While this example is silly and artificial, it is based on a real issue from @tiagoantao using fastqsangergz rather than fastqsanger.gz https://github.com/galaxyproject/tools-iuc/issues/1323#issuecomment-303446756

[jmchilton]

Also mentioned in #13 - happy to have a separate issue for it though - thanks @peterjc.

[hexylena]

Just another datapoint for the importance of this issue, we have 30k fastqsangars in our db:

extension	count	ok
fastqsanger	451645	:heavy_check_mark:
fastqsanger.gz	190145	:heavy_check_mark:
fastq	38542	:heavy_check_mark:
fastqsangar	29168	:heavy_multiplication_x:
fastq.gz	8248	:heavy_check_mark:
fastqillumina.gz	2350	:heavy_check_mark:
fastqcssanger.gz	1173	:heavy_check_mark:
fastqcssanger	804	:heavy_check_mark:
fastqillumina	779	:heavy_check_mark:
fastqsanger.bz2	637	:heavy_check_mark:
fastqsanger.	179	:heavy_multiplication_x:
fastqsolexa	132	:heavy_check_mark:
fastq2	73	:heavy_multiplication_x:
fastq.bz2	61	:heavy_check_mark:
fastqcssanger.bz2	40	:heavy_check_mark:
fastqillumina.bz2	18	:heavy_check_mark:
fastq.	7	:heavy_multiplication_x:
fastqsan	4	:heavy_multiplication_x:
fastqillumina.	2	:heavy_multiplication_x:
fastqsolexa.gz	1	:heavy_check_mark:
fastqsolexa.bz2	1	:heavy_check_mark:
fastqsolexa.	1	:heavy_multiplication_x: