diff bwa_mem.xml @ 1:ebb02ba5987c draft default tip

Rewrite of param handling. interPairEnd param moved to "paired" section. Add param for '-a' option. Remove basic parallelism tag, which does not work with multiple inputs (thanks Bjoern Gruening for the notice). Simplify Python code.

--- a/bwa_mem.xml	Tue Mar 18 07:49:22 2014 -0400
+++ b/bwa_mem.xml	Fri Mar 21 12:56:15 2014 -0400
@@ -1,26 +1,29 @@
-<tool id="bwa_mem" name="Map with BWA-MEM" version="0.7.7">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="0.8.0">
   <requirements>
     <requirement type="package" version="0.7.7">bwa</requirement>
   </requirements>
   <description></description>
-  <parallelism method="basic"></parallelism>
   <version_command>bwa 2&gt;&amp;1 | grep "Version: " | sed -e 's/Version: //'</version_command>
   <command interpreter="python">
     bwa_mem.py
       --threads="\${GALAXY_SLOTS:-1}"
       --fileSource="${genomeSource.refGenomeSource}"
-      #if $genomeSource.refGenomeSource == "history":
+      #if $genomeSource.refGenomeSource == "history"
         ##build index on the fly
         --ref="${genomeSource.ownFile}"
         --dbkey="${dbkey}"
-      #else:
+      #else
         ##use precomputed indexes
         --ref="${genomeSource.indices.fields.path}"
       #end if
 
       ## input file(s)
       --fastq="${paired.fastq}"
-      #if $paired.sPaired == "paired":
+      #if $paired.sPaired == "single"
+        #if $paired.interPairEnd
+          --interPairEnd
+        #end if
+      #else
         --rfastq="${paired.rfastq}"
       #end if
 
@@ -30,28 +33,60 @@
       ## run parameters
       --genAlignType="${paired.sPaired}"
       --params="${params.source_select}"
-      #if $params.source_select != "pre_set":
-        --minEditDistSeed="${params.minEditDistSeed}"
-        --bandWidth="${params.bandWidth}"
-        --offDiagonal="${params.offDiagonal}"
-        --internalSeeds="${params.internalSeeds}"
-        --seedsOccurrence="${params.seedsOccurrence}"
-        --mateRescue="${params.mateRescue}"
-        --skipPairing="${params.skipPairing}"
-        --seqMatch="${params.seqMatch}"
-        --mismatch="${params.mismatch}"
-        --gapOpen="${params.gapOpen}"
-        --gapExtension="${params.gapExtension}"
-        --clipping="${params.clipping}"
-        --unpairedReadpair="${params.unpairedReadpair}"
-        --interPairEnd="${params.interPairEnd}"
-        --minScore="${params.minScore}"
-        --mark="${params.mark}"
+      #if $params.source_select != "pre_set"
+        #if str($params.minEditDistSeed)
+          --minSeedLength ${params.minEditDistSeed}
+        #end if
+        #if str($params.bandWidth)
+          --bandWidth ${params.bandWidth}
+        #end if
+        #if str($params.offDiagonal)
+          --offDiagonal ${params.offDiagonal}
+        #end if
+        #if str($params.internalSeeds)
+          --internalSeeds ${params.internalSeeds}
+        #end if
+        #if str($params.seedsOccurrence)
+          --seedsOccurrence ${params.seedsOccurrence}
+        #end if
+        #if $params.mateRescue
+          --mateRescue
+        #end if
+        #if $params.skipPairing
+          --skipPairing
+        #end if
+        #if str($params.seqMatch)
+          --seqMatch ${params.seqMatch}
+        #end if
+        #if str($params.mismatch)
+          --mismatch ${params.mismatch}
+        #end if
+        #if str($params.gapOpen)
+          --gapOpen ${params.gapOpen}
+        #end if
+        #if str($params.gapExtension)
+          --gapExtension ${params.gapExtension}
+        #end if
+        #if $params.clipping
+          --clipping "${params.clipping}"
+        #end if
+        #if str($params.unpairedReadpair)
+          --unpairedReadpair ${params.unpairedReadpair}
+        #end if
+        #if str($params.minScore)
+          --minScore ${params.minScore}
+        #end if
+        #if $params.outputAll
+          --outputAll
+        #end if
+        #if $params.mark
+          --mark
+        #end if
 
         #if $params.readGroup.specReadGroup == "yes"
           --rgid="${params.readGroup.rgid}"
           --rgsm="${params.readGroup.rgsm}"
-          --rgpl="${params.readGroup.rgpl}"
+          --rgpl ${params.readGroup.rgpl}
           --rglb="${params.readGroup.rglb}"
           --rgpu="${params.readGroup.rgpu}"
           --rgcn="${params.readGroup.rgcn}"
@@ -65,7 +100,9 @@
       #end if
 
       ## suppress output SAM header
-      --suppressHeader="${suppressHeader}"
+      #if $suppressHeader
+        --suppressHeader
+      #end if
   </command>
 
   <inputs>
@@ -88,11 +125,12 @@
     </conditional>
     <conditional name="paired">
       <param name="sPaired" type="select" label="Is this library mate-paired?">
-        <option value="single">Single-end</option>
+        <option value="single">Single-end or interleaved paired-end</option>
         <option value="paired">Paired-end</option>
       </param>
       <when value="single">
         <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
+        <param name="interPairEnd" type="boolean" checked="false" label="FASTQ file consists of interleaved paired-end sequences (-p)" />
       </when>
       <when value="paired">
         <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
@@ -106,43 +144,55 @@
       </param>
       <when value="pre_set" />
       <when value="full">
-        <param name="minEditDistSeed" type="integer" value="19" label="Minimum seed length" />
-        <param name="bandWidth" type="integer" value="100" label="Band width for banded alignment" />
-        <param name="offDiagonal" type="integer" value="100" label="off-diagonal X-dropoff" />
-        <param name="internalSeeds" type="float" value="1.5" label="look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]" />
-        <param name="seedsOccurrence" type="integer" value="10000" label="skip seeds with more than INT occurrences" />
-        <param name="mateRescue" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skip seeds with more than INT occurrences" />
-        <param name="skipPairing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skpe pairing, mate rescue performed unless -S also in use" />
-        <param name="seqMatch" type="integer" value="1" label="score of a sequence match" />
-        <param name="mismatch" type="integer" value="4" label="penalty for a mismatch" />
-        <param name="gapOpen" type="integer" value="6" label="gap open penalty" />
-        <param name="gapExtension" type="text" value="None" label="gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]" />
-        <param name="clipping" type="integer" value="5" label="penalty for clipping" />
-        <param name="unpairedReadpair" type="integer" value="17" label="penalty for an unpaired read pair" />
-        <param name="interPairEnd" type="boolean" truevalue="True" falsevalue="False" checked="False" label="first query file consists of interleaved paired-end sequences" />
-        <param name="minScore" type="integer" value="30" label="minimum score to output" />
-        <param name="mark" type="boolean" truevalue="True" falsevalue="False" checked="False" label="mark shorter split hits as secondary (for Picard/GATK compatibility)" />
-
+        <param name="minEditDistSeed" type="integer" value="19" optional="true" label="Minimum seed length (-k)" />
+        <param name="bandWidth" type="integer" value="100" optional="true" label="Band width for banded alignment (-w)" />
+        <param name="offDiagonal" type="integer" value="100" optional="true" label="Off-diagonal X-dropoff (-d)" />
+        <param name="internalSeeds" type="float" value="1.5" optional="true" label="Look for internal seeds inside a seed longer than the minimum seed length times this value (-r)" help="This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy" />
+        <param name="seedsOccurrence" type="integer" value="10000" optional="true" label="Skip seeds with more occurrences than this value (-c)" />
+        <param name="mateRescue" type="boolean" checked="false" label="Skip mate rescue (-S)" />
+        <param name="skipPairing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Skip pairing (-P)" help="In the paired-end mode, perform Smith-Waterman to rescue missing hits only, but do not try to find hits that fit a proper pair" />
+        <param name="seqMatch" type="integer" value="1" optional="true" label="Score for a sequence match (-A)" />
+        <param name="mismatch" type="integer" value="4" optional="true" label="Penalty for a mismatch (-B)" />
+        <param name="gapOpen" type="integer" value="6" optional="true" label="Gap open penalty (-O)" />
+        <param name="gapExtension" type="integer" value="1" optional="true" label="Gap extension penalty (-E)" help="A gap of length k costs {gap open penalty} + k*{this value}" />
+        <param name="clipping" type="text" value="5" optional="true" label="Penalty for clipping (-L)" help="When performing Smith-Waterman extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best Smith-Waterman score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best Smith-Waterman score; clipping penalty is not deduced. If two comma-separated numbers are provided, the first is for 5'-end clipping and second for 3'-end clipping">
+          <validator type="regex" message="Invalid clipping, format is INT[,INT]">\d+(,\d+)?$</validator>
+        </param>
+        <param name="unpairedReadpair" type="integer" value="17" optional="true" label="Penalty for an unpaired read pair (-U)" help="" />
+        <param name="minScore" type="integer" value="30" optional="true" label="Minimum score to output (-T)" />
+        <param name="outputAll" type="boolean" checked="false" label="Output all found alignments for single-end or unpaired paired-end reads (-a)" help="These alignments will be flagged as secondary alignments" />
+        <param name="mark" type="boolean" checked="false" label="Mark shorter split hits as secondary (-M)" help="For Picard/GATK compatibility" />
         <conditional name="readGroup">
-          <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
+          <param name="specReadGroup" type="select" label="Specify the read group for this file? (-R)">
             <option value="yes">Yes</option>
             <option value="no" selected="True">No</option>
           </param>
           <when value="yes">
-            <param name="rgid" type="text" size="25" label="[Essential]Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG 
-tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group 
-IDs may be modified when merging SAM files in order to handle collisions." />
-            <param name="rgpl" type="text" size="25" label="[Essential]Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, 
-SOLID, HELICOS, IONTORRENT and PACBIO" />
-            <param name="rglb" type="text" size="25" label="[Essential]Library name (LB)" help="Required if RG specified" />
-            <param name="rgsm" type="text" size="25" label="[Essential]Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
+            <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions.">
+              <validator type="empty_field" />
+            </param>
+            <param name="rgpl" type="select" label="Platform/technology used to produce the reads (PL)">
+              <option value="CAPILLARY">CAPILLARY</option>
+              <option value="LS454">LS454</option>
+              <option value="ILLUMINA">ILLUMINA</option>
+              <option value="SOLID">SOLID</option>
+              <option value="HELICOS">HELICOS</option>
+              <option value="IONTORRENT">IONTORRENT</option>
+              <option value="PACBIO">PACBIO</option>
+            </param>
+            <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified">
+              <validator type="empty_field" />
+            </param>
+            <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced">
+              <validator type="empty_field" />
+            </param>
             <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
             <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
             <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
             <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" />
-            <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each 
-flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by 
-various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
+            <param name="rgfo" type="text" size="25" optional="true" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each flow of each read" help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
+              <validator type="regex">\*|[ACMGRSVTWYHKDBN]+$</validator>
+            </param>
             <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" />
             <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
             <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
@@ -151,7 +201,7 @@
         </conditional>
       </when>
     </conditional>
-    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
+    <param name="suppressHeader" type="boolean" checked="false" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
   </inputs>
 
   <outputs>