diff picard_FastqToSam.xml @ 0:4419e9980172 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_FastqToSam.xml	Thu Oct 23 12:03:34 2014 -0400
@@ -0,0 +1,229 @@
+<tool name="FastqToSam" id="picard_FastqToSam" version="1.122.0">
+  <description>convert Fastq data into unaligned BAM</description>
+  <requirements>
+    <requirement type="package" version="1.122.0">picard</requirement>
+  </requirements>
+  
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  
+  <command>
+    @java_options@
+    
+    java -jar \$JAVA_JAR_PATH/FastqToSam.jar
+    
+    #if str( $input_type.input_type_selector ) == "se":
+      FASTQ="${input_type.fastq}"
+    #elif str( $input_type.input_type_selector ) == "pe":
+      FASTQ="${input_type.fastq}"
+      FASTQ2="${input_type.fastq2}"
+    #else
+      FASTQ="${input_type.fastq.forward}"
+      FASTQ2="${input_type.fastq.reverse}"
+    #end if
+    
+    QUALITY_FORMAT="${quality_format}"
+    OUTPUT="${outFile}"
+    READ_GROUP_NAME="${read_group_name}"
+    SAMPLE_NAME="${sample_name}"
+    
+    #if str( $library_name ):
+      LIBRARY_NAME="${library_name}"
+    #end if
+    
+    #if str( $platform_unit ):
+      PLATFORM_UNIT="${platform_unit}"
+    #end if
+      
+    #if str( $platform ):
+      PLATFORM="${platform}"
+    #end if
+      
+    #if str( $sequencing_center ):
+      SEQUENCING_CENTER="${sequencing_center}"
+    #end if
+      
+    #if str( $predicted_insert_size ):
+      PREDICTED_INSERT_SIZE="${predicted_insert_size}"
+    #end if
+      
+    #if str( $comment ):
+      COMMENT="${comment}"
+    #end if
+      
+    #if str( $description ):
+      DESCRIPTION="${description}"
+    #end if
+      
+    #if str( $run_date ):
+      RUN_DATE="${run_date}"
+    #end if
+    
+    MIN_Q="${min_q}"
+    MAX_Q="${max_q}"
+    STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}"
+    ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}"
+    
+    SORT_ORDER=coordinate
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <conditional name="input_type">
+      <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
+        <option value="se">Single end (single dataset)</option>
+        <option value="pe">Paired end (two datasets)</option>
+        <option value="pc">Paired collection</option>
+      </param>
+      <when value="se">
+        <param name="fastq" type="data" format="fastq" label="Input fastq file for single end data" help="FASTQ"/>
+      </when>
+      <when value="pe">
+        <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
+        <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
+      </when>
+      <when value="pc">
+        <param name="fastq" type="data_collection" collection_type="paired" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
+      </when>
+    </conditional>
+      
+    <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
+      <option value="Standard" selected="True">Sanger (+33)</option>
+      <option value="Illumina">Illumina (+64)</option>
+      <option value="Solexa">Solexa (+66)</option>
+    </param>
+
+    <param name="read_group_name" type="text" size="20" value="A" label="Read group name" help="READ_GROUP_NAME"/>
+    <param name="sample_name" type="text" size="20" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
+    <param name="library_name" type="text" size="20" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
+    <param name="platform_unit" type="text" size="20" optional="True"  label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
+    <param name="platform" type="text" size="20" optional="True"  label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
+    <param name="sequencing_center" type="text" size="20" optional="True"  label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
+
+    <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
+    <param name="comment" type="text" size="20" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
+    <param name="description" type="text" size="20" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
+    <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
+    <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
+    <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
+    <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
+    <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
+    
+    <expand macro="VS" />
+    
+  </inputs> 
+  
+  <outputs>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="input_type_selector" value="pe" />
+      <param name="quality_format" value="Standard" />
+      <param name="read_group_name" value="A" />
+      <param name="sample_name" value="sample-a" />
+      <param name="library_name" value="A"/>
+      <param name="platform_unit" value="A"/>
+      <param name="platform" value="Illumina"/>
+      <param name="sequencing_center" value="A"/>
+      <param name="predicted_insert_size" value="300"/>
+      <param name="comment" value="A"/>
+      <param name="description" value="A"/>
+      <param name="run_date" value="2014-10-10"/>
+      <param name="min_q" value="0" />
+      <param name="max_q" value="93" />
+      <param name="strip_unpairied_mate_number" value="False" />
+      <param name="allow_and_ignore_empty_lines" value="False" />
+      <param name="validation_stringency" value="LENIENT"/>
+      <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" />
+      <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
+      <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
+    </test> 
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
+
+@dataset_collections@
+
+@RG@
+
+@description@
+
+  FASTQ=File
+  F1=File                       Input fastq file for single end data, or first read in paired end 
+                                data.  Required.
+                                
+  FASTQ2=File
+  F2=File                       Input fastq file for the second read of paired end data (if used).  
+
+  QUALITY_FORMAT=FastqQualityFormat
+  V=FastqQualityFormat          A value describing how the quality values are encoded in the fastq.  Either Solexa for 
+                                pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above 
+                                (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33.  
+                                If this value is not specified, the quality format will be detected automatically.  
+                                Default value: null. Possible values: {Solexa, Illumina, Standard} 
+
+  READ_GROUP_NAME=String
+  RG=String                     Read group name  Default value: A. 
+  
+  SAMPLE_NAME=String
+  SM=String                     Sample name to insert into the read group header  Required. 
+  
+  LIBRARY_NAME=String
+  LB=String                     The library name to place into the LB attribute in the read group header.
+  
+  PLATFORM_UNIT=String
+  PU=String                     The platform unit (often run_barcode.lane) to insert into the read group header.
+  
+  PLATFORM=String
+  PL=String                     The platform type (e.g. illumina, solid) to insert into the read group header.
+  
+  SEQUENCING_CENTER=String
+  CN=String                     The sequencing center from which the data originated.
+  
+  PREDICTED_INSERT_SIZE=Integer
+  PI=Integer                    Predicted median insert size, to insert into the read group header.
+  
+  COMMENT=String
+  CO=String                     Comment to include in the merged output file's header. 
+  
+  DESCRIPTION=String
+  DS=String                     Inserted into the read group header. 
+  
+  RUN_DATE=Iso8601Date
+  DT=Iso8601Date                Date the run was produced, to insert into the read group header. 
+  
+  MIN_Q=Integer                 Minimum quality allowed in the input fastq.  An exception will be thrown if a quality is 
+                                less than this value.  Default value: 0.
+                                
+  MAX_Q=Integer                 Maximum quality allowed in the input fastq.  An exception will be thrown if a quality is 
+                                greater than this value.  Default value: 93.
+  
+  STRIP_UNPAIRED_MATE_NUMBER=Boolean
+                                If true and this is an unpaired fastq any occurance of '/1' will be removed from the end 
+                                of a read name.  Default value: false.  Possible values: {true, false} 
+  
+  ALLOW_AND_IGNORE_EMPTY_LINES=Boolean
+                                Allow (and ignore) empty lines  Default value: false. Possible values: {true, false} 
+  
+
+@more_info@
+
+  </help>
+</tool>
+
+