| Previous changeset 1:ba7b0f11e470 (2021-06-18) Next changeset 3:f77f7a7f3b83 (2021-11-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 59c5c8edd0c2080d7685e312fee19de1da75097e" |
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modified:
salsa2.xml |
| b |
| diff -r ba7b0f11e470 -r ab5b7f6b7198 salsa2.xml --- a/salsa2.xml Fri Jun 18 20:29:33 2021 +0000 +++ b/salsa2.xml Thu Sep 23 19:36:12 2021 +0000 |
| b |
| @@ -5,7 +5,7 @@ </xrefs> <macros> <token name="@TOOL_VERSION@">2.3</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">salsa2</requirement> @@ -18,9 +18,18 @@ run_pipeline.py -a '$fasta_in' -l input.fasta.fai +#if $enzyme_conditional.enzyme_options == 'preconfigured': + #if $enzyme_conditional.preconfigured_enzymes == 'dovetail' + -e 'GATC' + #else if $enzyme_conditional.preconfigured_enzymes == 'arima1' + -e 'GATC,GANTC' + #else + -e 'GATC,GANTC,CTNAG,TTAA' + #end if +#else: + -e '${enzyme_conditional.manual_enzyme}' +#end if -b '$bed_file' --e '$enzyme' - #if str($cutoff): -c '$cutoff' #end if @@ -37,10 +46,25 @@ <param name="bed_file" type="data" format="bed" label="Bed alignment" help="Sorted by read names"/> <param name="cutoff" argument="-c" type="integer" min="1" label="Cutoff" optional="true" help="Minimum contig length to scaffold."/> <param name="gfa_file" argument="-g" type="data" format="gfa1,gfa2" optional="true" label="Sequence graphs" help="Sequence graphs encoded in GFA format."/> - <param name="enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)" - help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT')."> - <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator> - </param> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" type="select" label="Enzyme selection" help="TODO"> + <option value="preconfigured">Preconfigured restriction enzymes</option> + <option value="specific">Enter a specific sequence</option> + </param> + <when value="preconfigured"> + <param name="preconfigured_enzymes" type="select" multiple="true" label="Preconfigured enzymes"> + <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option> + <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option> + <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option> + </param> + </when> + <when value="specific"> + <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)" + help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT')."> + <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator> + </param> + </when> + </conditional> <param name="iter" argument="-i" type="integer" min="0" label="Iterations" optional="true" help="Number of iterations to run"/> </inputs> <outputs> @@ -53,17 +77,39 @@ <param name="length" value="test.fai"/> <param name="bed_file" value="test.bed"/> <param name="gfa_file" value="test.gfa1"/> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" value="specific"/> + <param name="manual_enzyme" value="GATC,GANTC"/> + </conditional> <param name="enzyme" value="GATC,GANTC"/> <param name="cutoff" value="1000"/> <param name="iter" value="3"/> <output name="scaffolds_fasta" file="out.fasta"/> <output name="scaffolds_agp" file="out.agp"/> </test> + <!--Test manual enzyme--> <test> <param name="fasta_in" value="test.fasta"/> <param name="bed_file" value="test.bed"/> <param name="gfa_file" value="test.gfa1"/> - <param name="enzyme" value="GATC,GANTC"/> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" value="specific"/> + <param name="manual_enzyme" value="GATC,GANTC"/> + </conditional> + <param name="cutoff" value="1000"/> + <param name="iter" value="3"/> + <output name="scaffolds_fasta" file="out.fasta"/> + <output name="scaffolds_agp" file="out.agp"/> + </test> + <!--Test predefined enzyme--> + <test> + <param name="fasta_in" value="test.fasta"/> + <param name="bed_file" value="test.bed"/> + <param name="gfa_file" value="test.gfa1"/> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" value="preconfigured"/> + <param name="preconfigured_enzymes" value="arima1"/> + </conditional> <param name="cutoff" value="1000"/> <param name="iter" value="3"/> <output name="scaffolds_fasta" file="out.fasta"/> |