diff microsatbed.xml @ 20:410144c7b2d6 draft

planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty

--- a/microsatbed.xml	Wed Jul 17 07:40:00 2024 +0000
+++ b/microsatbed.xml	Wed Jul 17 12:08:15 2024 +0000
@@ -4,6 +4,7 @@
     <requirement version="3.12.3" type="package">python</requirement>
     <requirement version="2.1.0" type="package">pyfastx</requirement>
     <requirement version="1.3.0" type="package">pytrf</requirement>
+    <requirement type="package" version="0.1.4">pybigtools</requirement>
   </requirements>
    <required_files>
       <include path="find_str.py"/>
@@ -26,6 +27,10 @@
     --bed '$bed'
     #if $mode_cond.mode == "SPECIFIC":
     --specific '$mode_cond.specific'
+    #elif $mode_cond.mode == "SPECIFICBW":
+    --bigwig
+    --winwidth '$mode_cond.winwidth'
+    --specific '$mode_cond.specific'
     #else:
       #if "MONO" in $mode_cond.subset:
       --mono
@@ -52,6 +57,10 @@
     --tetramin '$tetramin'
     --pentamin '$pentamin'
     --hexamin '$hexamin'
+    #if $mode_cond.mode == "SPECIFICBW":
+    --bigwig
+    --winwidth '$mode_cond.winwidth'
+    #end if
   #end if
 ]]></command>
   <inputs>
@@ -73,24 +82,41 @@
     <conditional name="mode_cond">
     <param name="mode" type="select" label="Select patterns by motif length; or provide a specific motif pattern to report?" help="Choose *By length:* or *By pattern:* to configure STR selection mode">
       <option selected="True" value="ALL">By length: Report all motifs of one or more specified lengths (1-6nt) as bed features</option>
+      <option value="ALLBW">By length as windowed bigwig: Report all motifs of one or more specified lengths (1-6nt) as windowed density</option>
       <option value="SPECIFIC">By motif: Report one or more specific motifs (such as TCA,GC) as bed features</option>
+      <option value="SPECIFICBW">By motif as windowed bigwig: Report one or more specific motifs (such as TCA,GC) as windowed density</option>
       <option value="NATIVE">All exact STR: use the pytrf findstr native command to a create csv, tsv or gtf output</option>
     </param>
     <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="TRI">All trimers (ACG,..)</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>
     </when>
+    <when value="ALLBW">
+      <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="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 type="integer" min="5" name="winwidth" label="Window with for estimating STR bigwig density" value="128"/>
+    </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"/>
     </when>
+    <when value="SPECIFICBW">
+      <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 type="integer" min="5" name="winwidth" label="Window with for estimating STR bigwig density" value="128"/>
+    </when>
     <when value="NATIVE">
       <param name="outformat" type="select" optional="false" label="Select the required output format" 
         help="Pytrf can create GFF, CSV or TSV output files. Documentation is linked in the help section below">
@@ -113,6 +139,8 @@
             <when input="mode_cond.outformat" value="gff" format="gff" />
             <when input="mode_cond.outformat" value="csv" format="csv" />
             <when input="mode_cond.outformat" value="tsv" format="tabular" />
+            <when input="mode_cond.mode" value="ALLBW" format="bigwig" />
+            <when input="mode_cond.mode" value="SPECIFICBW" format="bigwig" />
       </change_format>
     </data>
   </outputs>
@@ -168,6 +196,23 @@
       <param name="hexamin" value="2"/>
       <output name="bed" value="nativegff_sample" compare="diff" lines_diff="0"/>
     </test>
+    <test expect_num_outputs="1">
+      <conditional name="reference_genome">
+          <param name="genome_type_select" value="history"/>
+          <param name="fasta" value="humsamp.fa"/>
+      </conditional>
+      <conditional name="mode_cond">
+          <param name="mode" value="SPECIFICBW"/>
+          <param name="specific" value="GC"/>
+      </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_wig_sample" compare="sim_size" delta="10"/>
+    </test>
   </tests>
   <help><![CDATA[