changeset 12:f7ebcc9dfb86 draft

Deleted selected files

--- a/picard_ReorderSam.xml	Wed Jan 29 15:52:38 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,166 +0,0 @@
-<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
-  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
-  <command interpreter="python">
-    picard_wrapper.py
-      --input="${inputFile}"
-      #if $source.indexSource == "built-in"
-        --ref="${source.ref.fields.path}"
-      #else
-        --ref-file="${refFile}"
-        --species-name="${source.speciesName}"
-        --build-name="${source.buildName}"
-        --trunc-names="${source.truncateSeqNames}"
-      #end if
-      --allow-inc-dict-concord="${allowIncDictConcord}"
-      --allow-contig-len-discord="${allowContigLenDiscord}"
-      --output-format="${outputFormat}"
-      --output="${outFile}"
-      --tmpdir "${__new_file_path__}" 
-      -j "\$JAVA_JAR_PATH/ReorderSam.jar"
-  </command>
-  <inputs>
-    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
-           help="If empty, upload or import a SAM/BAM dataset." />
-    <conditional name="source">
-      <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">
-        <option value="built-in">Locally cached</option>
-        <option value="history">History</option>
-      </param>
-      <when value="built-in">
-        <param name="ref" type="select" label="Select a reference genome">
-          <options from_data_table="picard_indexes" />
-        </param>
-      </when>
-      <when value="history">
-        <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
-        <param name="speciesName" type="text" value="" label="Species name" />
-        <param name="buildName" type="text" value="" label="Build name" />
-        <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" />
-      </when>
-    </conditional>
-    <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
-    <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" />
-    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
-  </inputs>
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: reordered ${outputFormat}">
-      <change_format>
-        <when input="outputFormat" value="sam" format="sam" />
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <!-- Commands:
-      cp test-data/phiX.fasta .
-      samtools faidx phiX.fasta
-      java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
-      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input1.bam O=picard_RS_output1.bam REFERENCE=phiX.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-    -->
-      <param name="inputFile" value="picard_RS_input1.bam" />
-      <param name="indexSource" value="history" />
-      <param name="refFile" value="phiX.fasta" />
-      <param name="speciesName" value="phiX174" />
-      <param name="buildName" value="" />
-      <param name="truncateSeqNames" value="false" />
-      <param name="allowIncDictConcord" value="false" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="True" />
-      <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" />
-    </test>
-    <test>
-      <!-- Command:
-      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input2.sam O=picard_RS_output2.sam REFERENCE=/path/to/phiX/picard_index/phiX.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-      /path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict
-      -->
-      <param name="inputFile" value="picard_RS_input2.sam" />
-      <param name="indexSource" value="built-in" />
-      <param name="ref" value="phiX" />
-      <param name="allowIncDictConcord" value="false" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" />
-    </test>
-    <test>
-      <!-- Commands:
-      cp test-data/picard_RS_input4.fasta .
-      samtools faidx picard_RS_input4.fasta
-      java -jar CreateSequenceDictionary.jar R=picard_RS_input4.fasta O=picard_RS_input4.dict URI=picard_RS_input4.fasta TRUNCATE_NAMES_AT_WHITESPACE=true SPECIES=phiX174 GENOME_ASSEMBLY=phiX_buildBlah1.1
-      java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input3.bam O=picard_RS_output3.sam REFERENCE=picard_RS_input4.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false
-      picard_RS_input3.bam can be made from picard_RS_input3.sam
-      -->
-      <param name="inputFile" value="picard_RS_input3.bam" />
-      <param name="indexSource" value="history" />
-      <param name="refFile" value="picard_RS_input4.fasta" />
-      <param name="speciesName" value="phiX174" />
-      <param name="buildName" value="phiX_buildBlah1.1" />
-      <param name="truncateSeqNames" value="true" />
-      <param name="allowIncDictConcord" value="true" />
-      <param name="allowContigLenDiscord" value="false" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" />
-    </test>
-  </tests>
-  <help>
-
-.. class:: infomark
-
-**Purpose**
-
-Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is
-not the same as sorting as done by the SortSam tool, which sorts by either coordinate
-values or query name. The ordering in ReorderSam is based on exact name matching of
-contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are
-not included in the output.
-
-**Picard documentation**
-
-This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.
-
- .. _Picard-tools: http://www.google.com/search?q=picard+samtools
-
-------
-
-.. class:: infomark 
-
-**Inputs, outputs, and parameters**
-
-For the file that needs to be reordered, either a sam file or a bam file must be supplied.
-If a bam file is used, it must be coordinate-sorted. A reference file is also required,
-so either a fasta file should be supplied or a built-in reference can be selected.
-
-The output contains the same reads as the input file but the reads have been rearranged so
-they appear in the same order as the provided reference file. The tool will output either
-bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.
-
-The only extra parameters that can be set are flags for allowing incomplete dict concordance
-and allowing contig length discordance. If incomplete dict concordance is allowed, only a
-partial overlap of the bam contigs with the new reference sequence contigs is required. By
-default it is off, requiring a corresponding contig in the new reference for each read contig.
-If contig length discordance is allowed, contig names that are the same between a read and the
-new reference contig are allowed even if they have different lengths. This is usually not a
-good idea, unless you know exactly what you're doing. It's off by default.
-
-.. class:: warningmark
-
-**Warning on SAM/BAM quality**
-
-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
-flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
-to be the only way to deal with SAM/BAM that cannot be parsed.
-
-
-  </help>
-</tool>
-
-
-
-
-
-
-
-
-
-
-
-

--- a/picard_ReplaceSamHeader.xml	Wed Jan 29 15:52:38 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,115 +0,0 @@
-<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0">
-  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
-  <command interpreter="python">
-    picard_wrapper.py
-      --input "${inputFile}"
-      -o "${outFile}"
-      --header-file "${headerFile}"
-      --output-format "${outputFormat}"
-      -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar"
-      --tmpdir "${__new_file_path__}" 
-  </command>
-  <inputs>
-    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)"
-      help="If empty, upload or import a SAM/BAM dataset." />
-    <param format="bam,sam" name="headerFile" type="data" label="SAM/BAM to reader header from (SOURCE)"
-      help="If empty, upload or import a SAM/BAM dataset." />
-    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
-  </inputs>
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with replaced header">
-      <change_format>
-        <when input="outputFormat" value="sam" format="sam" />
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <!-- Command:
-      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.bam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output1.sam
-      picard_RSH_input1.bam can be made from picard_RSH_input1.sam
-      -->
-      <param name="inputFile" value="picard_input_tiny_coord.bam" ftype="bam" />
-      <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RSH_output1.sam" ftype="sam" />
-    </test>
-    <test>
-      <!-- Command:
-      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output2.sam
-      picard_RSH_input1.bam can be made from picard_RSH_input1.sam
-      -->
-      <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
-      <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
-      <param name="outputFormat" value="False" />
-      <output name="outFile" file="picard_RSH_output2.sam" ftype="sam" />
-    </test>
-    <test>
-      <!-- Command:
-      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.sam O=picard_RSH_output2.bam
-      -->
-      <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
-      <param name="headerFile" value="picard_RSH_input1.sam" ftype="sam" />
-      <param name="outputFormat" value="True" />
-      <output name="outFile" file="picard_RSH_output2.bam" ftype="bam" />
-    </test>
-  </tests>
-  <help>
-
-
-.. class:: infomark
-
-**Purpose**
-
-Replace Sam Header with the header from another sam file. The tool does not do any
-significant validation, so it's up to the user to make sure that the elements in
-the header are relevant and that the new header has all the required things.
-
-Replace the SAMFileHeader in a SAM file with the given header. Validation is
-minimal. It is up to the user to ensure that all the elements referred to in the
-SAMRecords are present in the new header. Sort order of the two input files must
-be the same.
-
-**Picard documentation**
-
-This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_.
-
- .. _Picard-tools: http://www.google.com/search?q=picard+samtools
-
-------
-
-.. class:: infomark
-
-**Inputs and outputs**
-
-Either a sam file or a bam file is required as the file whose header will be replaced.
-The header file is also required and can also be either sam or bam (it does not have
-to be the same type as the other file). In both cases, if a bam file is used, it must
-be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.
-
-The tool will output either bam (the default) or sam. Bam is recommended since it is smaller.
-
-.. class:: warningmark
-
-**Warning on SAM/BAM quality**
-
-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
-flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
-to be the only way to deal with SAM/BAM that cannot be parsed.
-
-
-
-  </help>
-</tool>
-
-
-
-
-
-
-
-
-
-
-
-

--- a/picard_SamToFastq.xml	Wed Jan 29 15:52:38 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,189 +0,0 @@
-<tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.1" force_history_refresh="True">
-  <description>creates a FASTQ file</description>
-  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
-  <!-- Dan Blankenberg -->
-  <command interpreter="python">picard_SamToFastq_wrapper.py
-    -p '
-    java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
-    -jar "\$JAVA_JAR_PATH/SamToFastq.jar"
-    INPUT="${input_sam}"
-    VALIDATION_STRINGENCY="LENIENT"
-    RE_REVERSE="${re_reverse}"
-    INCLUDE_NON_PF_READS="${include_non_pf_reads}"
-    #if str( $clipping_attribute ):
-        CLIPPING_ATTRIBUTE="${clipping_attribute}"
-    #end if
-    #if str( $clipping_action ):
-        CLIPPING_ACTION="${clipping_action}"
-    #end if
-    #if str( $read1_trim ):
-        READ1_TRIM="${read1_trim}"
-    #end if
-    #if str( $read1_max_bases_to_write ):
-        READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
-    #end if
-    INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
-    
-    #if str( $output_per_read_group_selector ) == 'per_sam_file':
-        ##OUTPUT_PER_RG=false
-        FASTQ="${output_fastq1}"
-        
-        #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired':
-            SECOND_END_FASTQ="${output_fastq2}"
-            #if str( $single_paired_end_type.read2_trim ): 
-                READ2_TRIM="${single_paired_end_type.read2_trim}"
-            #end if
-            #if str( $single_paired_end_type.read2_max_bases_to_write ):
-                READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
-            #end if
-        #end if
-        '
-    #else:
-        OUTPUT_PER_RG=true
-        #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired':
-            ' 
-            --read_group_file_2 "${output_fastq2}"
-            --file_id_2 "${output_fastq2.id}"
-            -p '
-            #if str( $single_paired_end_type.read2_trim ): 
-                READ2_TRIM="${single_paired_end_type.read2_trim}"
-            #end if
-            #if str( $single_paired_end_type.read2_max_bases_to_write ):
-                READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
-            #end if
-        #end if
-        '
-        --read_group_file_1 "${output_fastq1}"
-        --new_files_path "${__new_file_path__}"
-        --file_id_1 "${output_fastq1.id}"
-    #end if
-  </command>
-  <inputs>
-    <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" />
-    <param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." />
-    <param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." />
-    <param name="output_per_read_group_selector" type="select" label="Output per read group">
-      <option value="per_sam_file" selected="True">Per BAM/SAM file</option>
-      <option value="per_read_group">Per Read Group</option>
-    </param>
-    <conditional name="single_paired_end_type">
-      <param name="single_paired_end_type_selector" type="select" label="Single or Paired end">
-        <option value="single" selected="True">Single</option>
-        <option value="paired">Paired end</option>
-      </param>
-      <when value="single">
-        <!-- nothing yet -->
-      </when>
-      <when value="paired">
-        <param name="read2_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 2." />
-        <param name="read2_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 2 after trimming." />
-      </when>
-    </conditional>
-    <param name="re_reverse" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Re-reverse bases and qualities of reads on negative strand"/>
-    <param name="include_non_pf_reads" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Include non-PF reads from the SAM file into the output FASTQ files."/>
-    <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM record should be clipped" help="Leave blank for null" />
-    <param name="clipping_action" type="text" value="" label="The action that should be taken with clipped reads" help="'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Leave blank for null" />
-    <param name="include_non_primary_alignments" type="boolean" truevalue="true" falsevalue="false" checked="False" label="If true, include non-primary alignments in the output." help="Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments."/>
-    
-  </inputs>
-  <outputs>
-    <data format="fastqsanger" name="output_fastq1" label="${tool.name} on ${on_string}: FASTQ 1" />
-    <data format="fastqsanger" name="output_fastq2" label="${tool.name} on ${on_string}: FASTQ 2" >
-        <filter>single_paired_end_type['single_paired_end_type_selector'] == 'paired'</filter>
-    </data>
-  </outputs>
-  <tests>
-      <test>
-          <param name="input_sam" value="bfast_out1.sam" ftype="sam" />
-          <param name="output_per_read_group_selector" value="per_sam_file" />
-          <param name="single_paired_end_type_selector" value="single" />
-          <param name="read1_trim" value="" />
-          <param name="read1_max_bases_to_write" value="" />
-          <param name="re_reverse" value="True" />
-          <param name="include_non_pf_reads" value="False" />
-          <param name="clipping_action" value="" />
-          <param name="clipping_attribute" value="" />
-          <param name="include_non_primary_alignments" value="False" />
-          <output name="output_fastq1" file="random_phiX_1.fastqsanger"/> 
-      </test>
-      <test>
-          <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" />
-          <param name="output_per_read_group_selector" value="per_sam_file" />
-          <param name="single_paired_end_type_selector" value="paired" />
-          <param name="read1_trim" value="" />
-          <param name="read1_max_bases_to_write" value="" />
-          <param name="read2_trim" value="" />
-          <param name="read2_max_bases_to_write" value="" />
-          <param name="re_reverse" value="True" />
-          <param name="include_non_pf_reads" value="False" />
-          <param name="clipping_action" value="" />
-          <param name="clipping_attribute" value="" />
-          <param name="include_non_primary_alignments" value="False" />
-          <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
-          <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
-      </test>
-      <test>
-          <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" />
-          <param name="output_per_read_group_selector" value="per_read_group" />
-          <param name="single_paired_end_type_selector" value="paired" />
-          <param name="read1_trim" value="" />
-          <param name="read1_max_bases_to_write" value="" />
-          <param name="read2_trim" value="" />
-          <param name="read2_max_bases_to_write" value="" />
-          <param name="re_reverse" value="True" />
-          <param name="include_non_pf_reads" value="False" />
-          <param name="clipping_action" value="" />
-          <param name="clipping_attribute" value="" />
-          <param name="include_non_primary_alignments" value="False" />
-          <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
-          <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
-      </test>
-  </tests>
-  <help>
-**What it does**
-
-Picard: SamToFastq converts SAM files to FASTQ files.
-
-Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM file will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
-
-------
-
-Please cite the website "http://picard.sourceforge.net".
-
-------
-
-
-**Input formats**
-
-FastqToSam accepts SAM input files, see http://samtools.sourceforge.net for more details.
-
-------
-
-**Outputs**
-
-The output is in FASTQ format. If using Paired end data, 2 fastq files are created.
-
--------
-
-**FastqToSam settings**
-
-This is list of SamToFastq options::
-  
-  INPUT=File	Input SAM/BAM file to extract reads from Required.
-  FASTQ=File	Output fastq file (single-end fastq or, if paired, first end of the pair fastq). Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-  SECOND_END_FASTQ=File	Output fastq file (if paired, second end of the pair fastq). Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-  OUTPUT_PER_RG=Boolean	Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F)
-  OUTPUT_DIR=File	Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. Default value: null.
-  RE_REVERSE=Boolean	Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
-  INCLUDE_NON_PF_READS=Boolean	Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
-  CLIPPING_ATTRIBUTE=String	The attribute that stores the position at which the SAM record should be clipped Default value: null.
-  CLIPPING_ACTION=String	The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.
-  READ1_TRIM=Integer	The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.
-  READ1_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
-  READ2_TRIM=Integer	The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.
-  READ2_MAX_BASES_TO_WRITE=Integer	The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
-  INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean	If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} 
-
-
-  </help>
-</tool>