diff picard_FastqToSam.xml @ 8:e417b1d6288d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e

--- a/picard_FastqToSam.xml	Sun Nov 27 15:11:36 2016 -0500
+++ b/picard_FastqToSam.xml	Tue Dec 06 10:04:26 2016 -0500
@@ -6,10 +6,9 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
     picard
     FastqToSam
-    
+
     #if str( $input_type.input_type_selector ) == "se":
       FASTQ="${input_type.fastq}"
     #elif str( $input_type.input_type_selector ) == "pe":
@@ -19,54 +18,54 @@
       FASTQ="${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="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <conditional name="input_type">
@@ -86,7 +85,7 @@
         <param name="fastq" type="data_collection" collection_type="paired" format="fastq" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
       </when>
     </conditional>
-      
+
     <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
       <option value="Standard" selected="True">Sanger (+33)</option>
       <option value="Illumina">Illumina (+64)</option>
@@ -108,15 +107,15 @@
     <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
     <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
     <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
-    
+
     <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="input_type_selector" value="pe" />
@@ -139,9 +138,9 @@
       <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> 
+    </test>
   </tests>
-  
+
   <help>
 
 .. class:: infomark
@@ -157,62 +156,62 @@
 @description@
 
   FASTQ=File
-  F1=File                       Input fastq file for single end data, or first read in paired end 
+  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).  
+  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} 
+  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. 
-  
+  RG=String                     Read group name  Default value: A.
+
   SAMPLE_NAME=String
-  SM=String                     Sample name to insert into the read group header  Required. 
-  
+  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. 
-  
+  CO=String                     Comment to include in the merged output file's header.
+
   DESCRIPTION=String
-  DS=String                     Inserted into the read group header. 
-  
+  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 
+  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 
+
+  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} 
-  
+                                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} 
-  
+                                Allow (and ignore) empty lines  Default value: false. Possible values: {true, false}
+
 
 @more_info@