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Tidy up feature test tables
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@michaelbarton
michaelbarton committed Jul 27, 2016
1 parent d17272b commit fe9be9d
Showing 1 changed file with 16 additions and 18 deletions.
34 changes: 16 additions & 18 deletions features/biobox.feature
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Expand Up @@ -46,7 +46,7 @@ Feature: A CLI to run biobox-compatible Docker containers

Scenario Outline: Running a biobox short read assembler container
Given I copy the example data files:
| source | dest |
| source | dest |
| short_read_assembler/genome_paired_reads.fq.gz | reads.fq.gz |
When I run the command:
"""
Expand All @@ -57,8 +57,7 @@ Feature: A CLI to run biobox-compatible Docker containers
<ressources> \
--no-rm \
--input=<input> \
--output=<output> \
<args>
--output=<output>
"""
Then the stdout should be empty
And the stderr should be empty
Expand All @@ -67,12 +66,12 @@ Feature: A CLI to run biobox-compatible Docker containers
And the file "contigs.fa" should not be empty

Examples:
| assembler | ressources | args | input | output |
| bioboxes/velvet | | | reads.fq.gz | contigs.fa |
| bioboxes/velvet | | | $(realpath reads.fq.gz) | contigs.fa |
| bioboxes/velvet | | | reads.fq.gz | $(realpath .)/contigs.fa |
| bioboxes/velvet | --memory=1g --cpu-shares=512 | | reads.fq.gz | $(realpath .)/contigs.fa |
| bioboxes/velvet | -m 1g -c 512 | | $(realpath reads.fq.gz) | contigs.fa |
| assembler | ressources | input | output |
| bioboxes/velvet | | reads.fq.gz | contigs.fa |
| bioboxes/velvet | | $(realpath reads.fq.gz) | contigs.fa |
| bioboxes/velvet | | reads.fq.gz | $(realpath .)/contigs.fa |
| bioboxes/velvet | --memory=1g --cpu-shares=512 | reads.fq.gz | $(realpath .)/contigs.fa |
| bioboxes/velvet | -m 1g -c 512 | $(realpath reads.fq.gz) | contigs.fa |

Scenario Outline: Running a biobox assembler benchmark container
Given I create the directory "input"
Expand All @@ -93,19 +92,18 @@ Feature: A CLI to run biobox-compatible Docker containers
--no-rm \
--input-fasta=<input-fasta> \
<input-ref> \
--output=<output> \
<args>
--output=<output>
"""
Then the stdout should be empty
And the stderr should be empty
And the exit code should be 0
And the file "output/biobox.yaml" should exist
And the file "output/biobox.yaml" should not be empty
Examples:
| benchmark | args | ressources | input-fasta | input-ref | output |
| bioboxes/quast | | | $(realpath input/assembly.fasta) | --input-ref=$(realpath input/references) | $(realpath output) |
| bioboxes/quast | | | input/assembly.fasta | --input-ref=input/references | output |
| bioboxes/quast | | | input/assembly.fasta | | output |
| bioboxes/quast | | --memory=1g --cpu-shares=512 | $(realpath input/assembly.fasta) | --input-ref=$(realpath input/references) | $(realpath output) |
| bioboxes/quast | | -m 1g -c 512 | input/assembly.fasta | --input-ref=input/references | output |
| bioboxes/quast | | -m 1g -c 512 | input/assembly.fasta | | output |
| benchmark | ressources | input-fasta | input-ref | output |
| bioboxes/quast | | $(realpath input/assembly.fasta) | --input-ref=$(realpath input/references) | $(realpath output) |
| bioboxes/quast | | input/assembly.fasta | --input-ref=input/references | output |
| bioboxes/quast | | input/assembly.fasta | | output |
| bioboxes/quast | --memory=1g --cpu-shares=512 | $(realpath input/assembly.fasta) | --input-ref=$(realpath input/references) | $(realpath output) |
| bioboxes/quast | -m 1g -c 512 | input/assembly.fasta | --input-ref=input/references | output |
| bioboxes/quast | -m 1g -c 512 | input/assembly.fasta | | output |

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