Mercurial > repos > nml > bio_hansel
changeset 6:5a42e475436e draft
planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty
| author | nml |
|---|---|
| date | Thu, 22 Feb 2018 12:21:08 -0500 |
| parents | 6396d043667b |
| children | af59ac462926 |
| files | bio_hansel.xml |
| diffstat | 1 files changed, 17 insertions(+), 14 deletions(-) [+] |
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--- a/bio_hansel.xml Wed Feb 21 12:13:32 2018 -0500 +++ b/bio_hansel.xml Thu Feb 22 12:21:08 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="bio_hansel" name="Bio Hansel" version="1.2.0"> +<tool id="bio_hansel" name="Bio Hansel" version="1.2.1"> <description>SNV Subtyping with genome assemblies or reads</description> <requirements> <requirement type="package" version="1.2.0">bio_hansel</requirement> @@ -53,7 +53,7 @@ ## Use Json output #if $dev_args.use_json == "yes": - --json + --json #end if #if $kmer_vals.kmer_min @@ -80,6 +80,10 @@ --max-intermediate-tiles $qc_vals.max_intermediate_tiles #end if + #if $qc_vals.low_coverage_warning + --low-cov-warning $qc_vals.low_coverage_warning + #end if + ## Adding more parameters to the command. -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab @@ -101,10 +105,8 @@ #elif $data_type.type =="paired": -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq - #end if - ]]></command> <inputs> <conditional name="data_type"> @@ -147,26 +149,27 @@ <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/> <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> + <param name="low_coverage_warning" argument="--low-cov-warning" optional="True" type="integer" min="0" label="QC: Overall tile coverage below this value will trigger a low coverage warning" value="20" help="default = 20"/> </section> <section name="dev_args" title="Developer Options" expanded="False"> - <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details"> - <option value="no">no</option> - <option value="yes">yes</option> - </param> - </section> + <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details"> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + </section> </inputs> <outputs> <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json"> - <filter>dev_args['use_json'] == "yes"</filter> - </data> + <filter>dev_args['use_json'] == "yes"</filter> + </data> <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json"> - <filter>dev_args['use_json'] == "yes"</filter> + <filter>dev_args['use_json'] == "yes"</filter> </data> <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json"> - <filter>dev_args['use_json'] == "yes"</filter> + <filter>dev_args['use_json'] == "yes"</filter> </data> </outputs> <tests> @@ -325,4 +328,4 @@ } }</citation> </citations> -</tool> \ No newline at end of file +</tool>