Mercurial > repos > fubar > microsatbed
diff microsatbed.xml @ 17:264d79548d19 draft
planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
| author | fubar |
|---|---|
| date | Wed, 17 Jul 2024 06:08:33 +0000 |
| parents | ee773bbde3c3 |
| children | 607620f93b4c |
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--- a/microsatbed.xml Wed Jul 17 05:08:00 2024 +0000 +++ b/microsatbed.xml Wed Jul 17 06:08:33 2024 +0000 @@ -12,9 +12,9 @@ <command><![CDATA[ #if $mode_cond.mode == "NATIVE": #if $reference_genome.genome_type_select == "history": - pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta}' + pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta}' #else: - pytrf findstr -f '$mode_cond.outformat' -o $bed -r $mode_cond.monomin $mode_cond.dimin $mode_cond.trimin $mode_cond.tetramin $mode_cond.pentamin $mode_cond.hexamin '${reference_genome.fasta.fields.path}' + pytrf findstr -f '$mode_cond.outformat' -o $bed -r $monomin $dimin $trimin $tetramin $pentamin $hexamin '${reference_genome.fasta.fields.path}' #end if #else: python '${__tool_directory__}/find_str.py' @@ -26,7 +26,12 @@ --bed '$bed' #if $mode_cond.mode == "SPECIFIC": --specific '$mode_cond.specific' - --minreps '$mode_cond.minreps' + --monomin '$monomin' + --dimin '$dimin' + --trimin '$trimin' + --tetramin '$tetramin' + --pentamin '$pentamin' + --hexamin '$hexamin' #else: #if "MONO" in $mode_cond.subset: --mono @@ -46,12 +51,12 @@ #if "HEXA" in $mode_cond.subset: --hexa #end if - --monomin '$mode_cond.monomin' - --dimin '$mode_cond.dimin' - --trimin '$mode_cond.trimin' - --tetramin '$mode_cond.tetramin' - --pentamin '$mode_cond.pentamin' - --hexamin '$mode_cond.hexamin' + --monomin '$monomin' + --dimin '$dimin' + --trimin '$trimin' + --tetramin '$tetramin' + --pentamin '$pentamin' + --hexamin '$hexamin' #end if #end if ]]></command> @@ -80,26 +85,17 @@ <when value="ALL"> <param name="subset" type="select" multiple="true" optional="false" label="Select at least 1 specific motif length to report" help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more"> - <option value="DI" selected="true">All dimers (AC,AG,AT,...)</option> - <option value="TRI">All trimers (ACG,..)</option> - <option value="TETRA">All tetramers (ACGT,..)</option> - <option value="PENTA">All pentamers (ACGTC,..)</option> - <option value="HEXA">All hexamers (ACGTCG,..)</option> - <option value="MONO">All monomers (A,C...). Warning! Can produce overwhelming numbers of bed features</option> + <option value="DI" selected="true">All dimers (AC,AG,AT,...)</option> + <option value="TRI">All trimers (ACG,..)</option> + <option value="TETRA">All tetramers (ACGT,..)</option> + <option value="PENTA">All pentamers (ACGTC,..)</option> + <option value="HEXA">All hexamers (ACGTCG,..)</option> + <option value="MONO">All monomers (A,C...). Warning! Can produce overwhelming numbers of bed features</option> </param> - <param name="dimin" type="integer" value="2" min="1" label="Minimum number of repeats for dimers"/> - <param name="trimin" type="integer" value="2" min="2" label="Minimum number of repeats for trimers"/> - <param name="tetramin" type="integer" value="2" min="2" label="Minimum number of repeats for tetramers"/> - <param name="pentamin" type="integer" value="2" min="2" label="Minimum number of repeats for pentamers"/> - <param name="hexamin" type="integer" value="2" min="2" label="Minimum number of repeats for hexamers"/> - <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/> </when> <when value="SPECIFIC"> <param name="specific" type="text" label="Supply a specific motif pattern. Separate multiple patterns with commas such as GA,GC" help="Make bed features only for the nominated specific motifs." optional="false"/> - <param name="minreps" type="integer" value="2" min="1" label="Minimum number of repeats of each of these motifs to report" - help="Short tandem repeats require 2 or more consecutive motifs by definition. WARNING: If monomers are included, every single matching base will be reported as a STR if minimum repeats = 1!" - optional="false"/> </when> <when value="NATIVE"> <param name="outformat" type="select" optional="false" label="Select the required output format" @@ -108,14 +104,14 @@ <option value="csv">Comma separated values</option> <option value="tsv" selected="true">Tab separated values</option> </param> - <param name="monomin" type="integer" value="2" min="2" label="Minimum number of repeats for monomers"/> - <param name="dimin" type="integer" value="2" min="1" label="Minimum number of repeats for dimers"/> - <param name="trimin" type="integer" value="2" min="2" label="Minimum number of repeats for trimers"/> - <param name="tetramin" type="integer" value="2" min="2" label="Minimum number of repeats for tetramers"/> - <param name="pentamin" type="integer" value="2" min="2" label="Minimum number of repeats for pentamers"/> - <param name="hexamin" type="integer" value="2" min="2" label="Minimum number of repeats for hexamers"/> </when> </conditional> + <param type="integer" min="2" name="monomin" value="10"/> + <param type="integer" min="1" name="dimin" value="3"/> + <param type="integer" min="2" name="trimin" value="2"/> + <param type="integer" min="2" name="tetramin" value="2"/> + <param type="integer" min="2" name="pentamin" value="2"/> + <param type="integer" min="2" name="hexamin" value="2"/> </inputs> <outputs> <data name="bed" format="bed" label="STR from $fasta.element_identifier" hidden="false"> @@ -135,12 +131,13 @@ <conditional name="mode_cond"> <param name="mode" value="ALL"/> <param name="subset" value="DI,TRI,TETRA,PENTA,HEXA"/> - <param name="dimin" value="2"/> - <param name="trimin" value="2"/> - <param name="tetramin" value="2"/> - <param name="pentamin" value="2"/> - <param name="hexamin" value="2"/> </conditional> + <param name="monomin" value="20"/> + <param name="dimin" value="2"/> + <param name="trimin" value="2"/> + <param name="tetramin" value="2"/> + <param name="pentamin" value="2"/> + <param name="hexamin" value="2"/> <output name="bed" value="bed_sample" compare="diff" lines_diff="0"/> </test> <test expect_num_outputs="1"> @@ -151,8 +148,13 @@ <conditional name="mode_cond"> <param name="mode" value="SPECIFIC"/> <param name="specific" value="GC"/> - <param name="minreps" value="2"/> </conditional> + <param name="monomin" value="20"/> + <param name="dimin" value="1"/> + <param name="trimin" value="20"/> + <param name="tetramin" value="20"/> + <param name="pentamin" value="20"/> + <param name="hexamin" value="20"/> <output name="bed" value="dibed_sample" compare="diff" lines_diff="0"/> </test> <test expect_num_outputs="1"> @@ -163,13 +165,13 @@ <conditional name="mode_cond"> <param name="mode" value="NATIVE"/> <param name="outformat" value="gff"/> - <param name="monomin" value="20"/> - <param name="dimin" value="10"/> - <param name="trimin" value="5"/> - <param name="tetramin" value="4"/> - <param name="pentamin" value="4"/> - <param name="hexamin" value="2"/> </conditional> + <param name="monomin" value="20"/> + <param name="dimin" value="10"/> + <param name="trimin" value="5"/> + <param name="tetramin" value="4"/> + <param name="pentamin" value="4"/> + <param name="hexamin" value="2"/> <output name="bed" value="nativegff_sample" compare="diff" lines_diff="0"/> </test> </tests>