# HG changeset patch
# User qfab
# Date 1409271595 14400
# Node ID fc523597d86d343a0d77b14052121f53437f8fb1
# Parent  c9d76b53903a844e5b34f48f9379cc1f14f5263a
Uploaded

diff -r c9d76b53903a -r fc523597d86d bowtie_for_fasta_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_for_fasta_wrapper.xml	Thu Aug 28 20:19:55 2014 -0400
@@ -0,0 +1,192 @@
+<tool id="bowtie_for_fasta_wrapper" name="Map with Bowtie for Fasta" version="1.1.2">
+  <requirements>
+    <requirement type='package' version="0.12.7">bowtie</requirement>
+  </requirements>
+  <description>Fasta File</description>
+  <parallelism method="basic"></parallelism>
+  <command interpreter="python">
+  bowtie_for_fasta_wrapper.py
+  ## Hackish setting of number of threads
+  --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 "${maqerr}"
+  ## The query input files
+  ## Inputs
+  --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
+  --genomeSource="${refGenomeSource.genomeSource}"
+  #if $refGenomeSource.genomeSource == "history":
+    ##index already exists
+    #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
+      ##user previously built
+      --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
+      --do_not_build_index
+    #else:
+      ##build index on the fly
+      --ref="${refGenomeSource.ownFile}"
+      --indexSettings="${refGenomeSource.indexParams.indexSettings}"
+      #if $refGenomeSource.indexParams.indexSettings == "indexFull":
+        --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
+        #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
+          --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
+          --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
+          --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
+          --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
+        #end if
+        --inodc="${refGenomeSource.indexParams.nodc}"
+        --inoref="${refGenomeSource.indexParams.noref}"
+        --ioffrate="${refGenomeSource.indexParams.offrate}"
+        --iftab="${refGenomeSource.indexParams.ftab}"
+        --intoa="${refGenomeSource.indexParams.ntoa}"
+        --iendian="${refGenomeSource.indexParams.endian}"
+        --iseed="${refGenomeSource.indexParams.seed}"
+        --icutoff="${refGenomeSource.indexParams.cutoff}"
+      #end if
+    #end if
+  #else
+    ##use pre-built index
+    --ref="${refGenomeSource.index.fields.path}"
+  #end if
+  ##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">
+      <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>
+      </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">
+          <options from_data_table="bowtie_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
+        <conditional name="indexParams">
+          <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
+            <option value="indexPreSet">Default</option>
+            <option value="indexFull">Set your own</option>
+          </param> 
+          <when value="indexPreSet" />
+          <when value="indexFull">
+            <conditional name="autoBehavior">
+              <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv">
+                <option value="auto">Automatic behavior</option>
+                <option value="set">Set values (sets --noauto and allows others to be set)</option>
+              </param>
+              <when value="auto" />
+              <when value="set">
+                <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)">
+                  <option value="unpacked">Use regular representation</option>
+                  <option value="packed">Use packed representation</option>
+                </param>
+                <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" />
+                <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" />
+                <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
+              </when>
+            </conditional>
+            <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)">
+              <option value="dc">Use difference-cover sample</option>
+              <option value="nodc">Disable difference-cover sample</option>
+            </param>
+            <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
+              <option value="ref">Build all index files</option>
+              <option value="noref">Do not build paired-end alignment index files</option>
+            </param>
+            <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" />
+            <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" />
+            <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
+              <option value="no">Do not convert Ns</option>
+              <option value="yes">Convert Ns to As</option>
+            </param>
+            <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture">
+              <option value="little">Little</option>
+              <option value="big">Big</option>
+            </param> 
+            <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
+            <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" />
+          </when>  <!-- indexFull -->
+        </conditional>  <!-- indexParams -->
+      </when>  <!-- history -->
+    </conditional>  <!-- refGenomeSource -->
+    <param name="sInput1" type="data" format="fasta" label="FASTA file" />
+	<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>
+    <data format="sam" name="samoutput" label="${tool.name} on ${on_string}: SAM">
+	<filter>outformat == "sam"</filter>
+      <actions>
+        <conditional name="refGenomeSource.genomeSource">
+          <when value="indexed">
+            <action type="metadata" name="dbkey">
+              <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+              </option>
+            </action>
+          </when>
+          <when value="history">
+            <action type="metadata" name="dbkey">
+              <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+            </action>
+          </when>
+        </conditional>
+      </actions>
+    </data>
+    <data format="tabular" name="fastaoutput" label="${tool.name} on ${on_string}: TAB">
+	<filter>outformat == "tab"</filter>
+        <conditional name="refGenomeSource.genomeSource">
+          <when value="indexed">
+            <action type="metadata" name="dbkey">
+              <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+              </option>
+            </action>
+          </when>
+          <when value="history">
+            <action type="metadata" name="dbkey">
+              <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+            </action>
+          </when>
+        </conditional>
+    </data>   
+  </outputs>
+</tool>