# HG changeset patch
# User qfab
# Date 1409271715 14400
# Node ID 89563c2b1f7140f22dff826601e5906bd8fdd1f7
# Parent  d33922d2b6e0b45405a6bf0f525156db424f45da
Uploaded

diff -r d33922d2b6e0 -r 89563c2b1f71 bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml
--- a/bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml	Thu Aug 28 20:20:48 2014 -0400
+++ b/bowtie_for_fasta-254d8bd5d21a/bowtie_for_fasta_wrapper.xml	Thu Aug 28 20:21:55 2014 -0400
@@ -7,27 +7,20 @@
   <command interpreter="python">
   bowtie_for_fasta_wrapper.py
   ## Hackish setting of number of threads
-    --threads="4"
-  ## Output  
-  #if str( $outformat) == "sam":
-    -S "true"
-    --output "${samoutput}"
-  #else:
-    -S "false"
-    --output "${taboutput}"
-  #end if
-
-
-##    #if $output_unmapped_reads_l
-##      --output_unmapped_reads="${output_unmapped_reads_l}"
-##    #end if
-##    #if $output_suppressed_reads_l
-##      --output_suppressed_reads="${output_suppressed_reads_l}"
-##    #end if
-##      --galaxy_input_format="${singlePaired.sInput1.ext}"
+  --threads="4"
+  ## valid Alignments according to the following policy
+  -n "${validal}"
+  ## Suppress all alignments for a particular read or pair if more
+  -m "${suppal}"
+  ## Report up to int valid alignments
+  -k "${reportvalal}"
+  ## The "seed length"
+  -l "${seedlength}"
+  ## Mismatched
+  -e "${maqerr}"
+  ## The query input files
   ## Inputs
   --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
-##  --suppressHeader="${suppressHeader}"
   --genomeSource="${refGenomeSource.genomeSource}"
   #if $refGenomeSource.genomeSource == "history":
     ##index already exists
@@ -61,31 +54,16 @@
     ##use pre-built index
     --ref="${refGenomeSource.index.fields.path}"
   #end if
-  --input1="${sInput1}"
-  --params="${Params.sSettingsType}"
-  --mismatchQual="${sMismatchQual}"
-  --mismatchSeed="${sMismatchSeed}"
-  --seedLen="${sSeedLen}"
-  --suppressAlign="${sSuppressAlign}"
-  --valAlign="${sValAlign}"
-  #unless $Params.sSettingsType:
-     --skip="${Params.sSkip}"
-     --alignLimit="${Params.sAlignLimit}"
-     --trimH="${Params.sTrimH}"
-     --trimL="${Params.sTrimL}"
-     --rounding="${Params.sRounding}"
-     --maqSoapAlign="${Params.sMaqSoapAlign}"
-     --tryHard="${Params.sTryHard}"
-     --best="${Params.sBestOption.sBest}"
-     #if $Params.sBestOption.sBest == "doBest":
-       --maxBacktracks="${Params.sBestOption.sdMaxBacktracks}"
-       --strata="${Params.sBestOption.sdStrata}"
-     #else:
-     --maxBacktracks="${Params.sBestOption.snMaxBacktracks}"
-     #end if
-     --offrate="${Params.sOffrate}"
-     --seed="${Params.sSeed}"
-  #end unless
+  ##FASTA file
+  -f "${sInput1}"
+  ## Output format
+  #if str( $outformat) == "sam"
+    -S "true"
+    -o "${samoutput}"
+  #else
+    -S "false"
+    -o "${fastaoutput}"
+  #end if
   </command>
   <inputs>
     <conditional name="refGenomeSource">
@@ -151,63 +129,29 @@
       </when>  <!-- history -->
     </conditional>  <!-- refGenomeSource -->
     <param name="sInput1" type="data" format="fasta" label="FASTA file" />
-    <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
-    <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="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" />
-    <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
-    <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
-    <param name="outformat" size="" type="select" label="Output format">
-      <option value="tab">TABULAR</option>
-      <option value="sam">SAM</option>
-    </param>
-
-    <conditional name="Params">
-     <param name="sSettingsType" type="boolean" checked="true" label="Default settings to use" help="For most mapping needs use Commonly used settings. If you want full control uncheck this box"/>
-    <when value="true"></when>
-    <when value="false">
-    <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
-    <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
-    <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
-    <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
-    <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
-	<option value="round">Round to nearest 10</option>
-        <option value="noRound">Do not round to nearest 10</option>
-    </param>
-    <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
-    <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
-      <option value="noTryHard">Do not try hard</option>
-      <option value="doTryHard">Try hard</option>
-    </param>
-    <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>
-    </param>
-    <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)" />
-      <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">
-        <option value="noBest">Do not use best</option>
-        <option value="doBest">Use best</option>
-        </param>
-        <when value="noBest">
-          <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
-        </when>
-        <when value="doBest">
-          <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
-          <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)">
-          <option value="noStrata">Do not use strata option</option>
-          <option value="doStrata">Use strata option</option>
-          </param>
-        </when>
-      </conditional> <!-- bestOption -->
-      <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 -->
-    </conditional>
+	<param name="validal" size="30" type="integer" value="0" label="Number of valid alignments (-n)" >
+			<validator type="empty_field" message="Enter a valid number of alignements (default 0)"/>
+	</param>
+	<param name="suppal" size="30" type="integer" value="1" label="Suppress all alignements if more than" help="Suppress all alignments for a particular read or pair if more than int reportable alignments exist for it" >
+			<validator type="empty_field" message="Enter a valid number"/>
+	</param>
+	<param name="reportvalal" size="30" type="integer" value="1" label="Report up to int valid alignments per read">
+			<validator type="empty_field" message="Enter a valid number"/>
+	</param>
+	<param name="seedlength" size="30" type="integer" value="36" label="The seed length">
+			<validator type="empty_field" message="Enter a valid number"/>
+	</param>
+	<param name="maqerr" size="30" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched">
+			<validator type="empty_field" message="Enter a valid number"/>
+	</param>
+	<param name="outformat" size="" type="select" label="Output format">
+		<option value="tab">TABULAR</option>
+        <option value="sam">SAM</option>
+	</param>
   </inputs>
-  <outputs>        
+  <outputs>
     <data format="sam" name="samoutput" label="${tool.name} on ${on_string}: SAM">
-    <filter>outformat == "sam"</filter>
+	<filter>outformat == "sam"</filter>
       <actions>
         <conditional name="refGenomeSource.genomeSource">
           <when value="indexed">
@@ -226,8 +170,8 @@
         </conditional>
       </actions>
     </data>
-    <data format="tabular" name="taboutput" label="${tool.name} on ${on_string}: TAB">
-    <filter>outformat == "tab"</filter>
+    <data format="tabular" name="fastaoutput" label="${tool.name} on ${on_string}: TAB">
+	<filter>outformat == "tab"</filter>
         <conditional name="refGenomeSource.genomeSource">
           <when value="indexed">
             <action type="metadata" name="dbkey">
@@ -243,6 +187,6 @@
             </action>
           </when>
         </conditional>
-    </data>
+    </data>   
   </outputs>
 </tool>