1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ba176739183d/ changeset: ba176739183d user: dan date: 2011-10-24 22:32:13 summary: Update for Sam to Fastq. affected #: 1 file
diff -r 0509a6aa2a7876648811b5b445ab7fcbbe982d32 -r ba176739183db096516eeb274b1120a38d9b6e5c tools/picard/picard_SamToFastq.xml --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -19,17 +19,17 @@ #end if INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments}
- #if str( $output_per_read_group.output_per_read_group_selector ) == 'per_sam_file': + #if str( $output_per_read_group_selector ) == 'per_sam_file': ##OUTPUT_PER_RG=false FASTQ="${output_fastq1}"
- #if str( $output_per_read_group.single_paired_end_type.single_paired_end_type_selector ) == 'paired': + #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired': SECOND_END_FASTQ="${output_fastq2}" - #if str( $output_per_read_group.single_paired_end_type.read2_trim ): - READ2_TRIM="${output_per_read_group.single_paired_end_type.read2_trim}" + #if str( $single_paired_end_type.read2_trim ): + READ2_TRIM="${single_paired_end_type.read2_trim}" #end if - #if str( $output_per_read_group.single_paired_end_type.read2_max_bases_to_write ): - READ2_MAX_BASES_TO_WRITE="${output_per_read_group.single_paired_end_type.read2_max_bases_to_write}" + #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: @@ -45,29 +45,22 @@ <param name="input_sam" type="data" format="sam" label="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." /> - <conditional name="output_per_read_group"> - <param name="output_per_read_group_selector" type="select" label="Output per read group"> - <option value="per_sam_file" selected="True">Per SAM file</option> - <option value="per_read_group">Per Read Group</option> - <validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator> + <param name="output_per_read_group_selector" type="select" label="Output per read group"> + <option value="per_sam_file" selected="True">Per SAM file</option> + <!-- <option value="per_read_group">Per Read Group</option> --> + <validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator> + </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="per_sam_file"> - <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> + <when value="single"> + <!-- nothing yet --></when> - <when value="per_read_group"> - <!-- Fix me --> + <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"/> @@ -80,7 +73,7 @@ <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>output_per_read_group['single_paired_end_type']['single_paired_end_type_selector'] == 'paired'</filter> + <filter>single_paired_end_type['single_paired_end_type_selector'] == 'paired'</filter></data></outputs><tests> @@ -141,20 +134,22 @@ **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}
-NPUT=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>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.