diff bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml @ 5:b300c15426f5 draft

Uploaded

--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml	Tue Mar 15 10:27:46 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml	Mon Mar 21 12:53:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="1.3">
+<tool id="bowtie_rRNA_removal_wrapper" name="Remove rRNA using Bowtie" version="1.4.0">
   <description></description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -156,7 +156,7 @@
     <conditional name="refGenomeSource">
       <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
         <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
+        <option value="history" selected="True">Use one from the history</option>
       </param>
       <when value="indexed">
         <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
@@ -248,6 +248,7 @@
               </when>
               <when value="vMode">
                 <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
+                <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
               </when>
             </conditional>
             <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
@@ -256,7 +257,7 @@
             </param>
             <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
               <option value="reverse">Align against the reverse-complement reference strand</option>
-              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
+              <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
             </param>
             <conditional name="sBestOption">
               <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
@@ -295,7 +296,7 @@
             <conditional name="sAllValAlignsOption">
               <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
                 <option value="noAllValAligns">Do not report all valid alignments</option>
-                <option value="doAllValAligns">Report all valid alignments</option>
+                <option value="doAllValAligns" selected="true">Report all valid alignments</option>
               </param>
               <when value="noAllValAligns">
                 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
@@ -304,7 +305,7 @@
             </conditional>
             <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
             <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
-            <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
+            <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Write all reads that could not be aligned to a file (--un)" />
             <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
             <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
           </when> <!-- full -->
@@ -339,7 +340,7 @@
             <conditional name="alignModeOption">
               <param name="alignMode" type="select" label="Alignment mode">
                 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
-                <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
+                <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
               </param>
               <when value="nMode">
                 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
@@ -352,6 +353,7 @@
               </when>
               <when value="vMode">
                 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
+                <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
               </when>
             </conditional>
             <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
@@ -361,7 +363,7 @@
             </param>
             <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
               <option value="reverse">Align against the reverse-complement reference strand</option>
-              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
+              <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
             </param>
             <conditional name="pBestOption">
               <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
@@ -402,7 +404,7 @@
             <conditional name="pAllValAlignsOption">
               <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
                 <option value="noAllValAligns">Do not report all valid alignments</option>
-                <option value="doAllValAligns">Report all valid alignments</option>
+                <option value="doAllValAligns" selected="True">Report all valid alignments</option>
               </param>
               <when value="noAllValAligns">
                 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
@@ -418,7 +420,7 @@
         </conditional> <!-- pParams -->
       </when> <!-- paired -->
     </conditional> <!-- singlePaired -->
-    <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
+    <param name="save_mapping_stats" type="boolean" checked="True" label="Save the bowtie mapping statistics to the history" />
     <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
   </inputs>
   <outputs>