| Previous changeset 0:71976cfc9022 (2017-12-04) Next changeset 2:a7093d5933a8 (2018-03-26) |
|
Commit message:
planemo upload for repository https://github.com/phac-nml/quasitools commit 1a2c7bac09d21d92533bc2ef31dd05c7ac41b39f |
|
modified:
hydra.xml |
| b |
| diff -r 71976cfc9022 -r 1abf6b32ecfd hydra.xml --- a/hydra.xml Mon Dec 04 10:25:26 2017 -0500 +++ b/hydra.xml Wed Dec 13 10:28:31 2017 -0500 |
| [ |
| @@ -5,10 +5,23 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ - quasitools hydra '$forward' + quasitools hydra + + ## Preparing file input. + #if $data_type.type == "paired": + + '$data_type.fastq_input1' + '$data_type.fastq_input2' - #if $reverse: - '$reverse' + #elif $data_type.type == "collection": + + '$data_type.fastq_input1.forward' + '$data_type.fastq_input1.reverse' + + #elif $data_type.type == "single": + + '$data_type.fastq_input1' + #end if #if $mutation_db: @@ -63,8 +76,23 @@ ]]></command> <inputs> - <param name="forward" type="data" format="fastq" optional="false" label="Forward read" /> - <param name="reverse" type="data" format="fastq" optional="true" label="Reverse read" help="Not required."/> + <conditional name="data_type"> + <param name="type" type="select" label="Specify the read type."> + <option value="single">Single-end Data</option> + <option value="paired">Paired-end Data</option> + <option value="collection">Collection Paired-end Data</option> + </param> + <when value="single"> + <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/> + </when> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/> + <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/> + </when> + <when value="collection"> + <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> + </when> + </conditional> <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." /> <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." /> @@ -90,7 +118,8 @@ </outputs> <tests> <test> - <param name="forward" value="forward.fastq" /> + <param name="type" value="single"/> + <param name="fastq_input1" value="forward.fastq" /> <output name="output_coverage"> <assert_contents> <has_text text="frame: 0" /> |