Mercurial > repos > devteam > picard
diff picard_SamToFastq.xml @ 13:7e6fd3d0f16e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
| author | devteam |
|---|---|
| date | Tue, 06 Dec 2016 10:04:41 -0500 |
| parents | 05087b27692a |
| children | 465cbb0cf2eb |
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--- a/picard_SamToFastq.xml Sun Nov 27 15:11:50 2016 -0500 +++ b/picard_SamToFastq.xml Tue Dec 06 10:04:41 2016 -0500 @@ -5,16 +5,17 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - + echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below) - + @java_options@ - + @symlink_element_identifier@ + picard SamToFastq - - INPUT="${inputFile}" - + + INPUT='$inputFile.element_identifier' + #if str( $output_per_rg ) == "true": OUTPUT_PER_RG=true OUTPUT_DIR=. @@ -25,34 +26,34 @@ #elif str( $output_per_rg ) == "false" and str( $interleave ) == "true": FASTQ=INTERLEAVED.fastq #end if - + RE_REVERSE="${re_reverse}" INTERLEAVE="${interleave}" INCLUDE_NON_PF_READS="${include_non_pf_reads}" CLIPPING_ATTRIBUTE="${clipping_attribute}" CLIPPING_ACTION="${clipping_action}" READ1_TRIM="${read1_trim}" - + #if int($read1_max_bases_to_write) > -1: READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" #end if - + READ2_TRIM="${read2_trim}" - + #if int($read2_max_bases_to_write) > -1: READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}" #end if - + INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" - - + + VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + ]]></command> <inputs> - + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/> <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/> @@ -65,18 +66,18 @@ <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/> <param name="read2_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 2 after trimming" help="READ2_MAX_BASES_TO_WRITE; 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=null (-1)"/> <param name="include_non_primary_alignments" type="boolean" label="If true, include non-primary alignments in the output" help="INCLUDE_NON_PRIMARY_ALIGNMENTS; 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=False"/> - + <expand macro="VS" /> - - </inputs> - + + </inputs> + <outputs> <!-- here dataset discovery is based on fact that if OUTPUT_PER_RG=true this tool automatically adds .fastq extension to emitted files --> <data format="txt" name="report" label="SamToFastq run" hidden="true"> <discover_datasets pattern="(?P<designation>.+)\.fastq" ext="fastqsanger" visible="true"/> </data> </outputs> - + <tests> <test> <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> @@ -90,7 +91,7 @@ <param name="read1_max_bases_to_write" value="-1"/> <param name="read2_trim" value="0" /> <param name="read2_max_bases_to_write" value="-1"/> - <param name="include_non_primary_alignments" value="false"/> + <param name="include_non_primary_alignments" value="false"/> <output name="report"> <assert_contents> <has_line line="BAM" /> @@ -99,8 +100,8 @@ </output> </test> </tests> - - + + <help> **Purpose** @@ -120,71 +121,71 @@ @description@ FASTQ=File - F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq). + F=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 - F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null. + F2=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) - + UNPAIRED_FASTQ=File - FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default + FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) - + OUTPUT_PER_RG=Boolean - OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is + OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) - + OUTPUT_DIR=File - ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. - Default value: null. - + ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. + Default value: null. + RE_REVERSE=Boolean - RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them - to fastq Default value: true. Possible values: {true, false} - + RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them + to fastq Default value: true. Possible values: {true, false} + INTERLEAVE=Boolean - INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe - which end it came from Default value: false. Possible values: {true, false} - + INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe + which end it came from Default value: false. Possible values: {true, false} + INCLUDE_NON_PF_READS=Boolean - NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes - filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. - Default value: false. Possible values: {true, false} - + NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes + filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. + Default value: false. Possible values: {true, false} + CLIPPING_ATTRIBUTE=String - CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default - value: null. - + CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default + value: null. + CLIPPING_ACTION=String - CLIP_ACT=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. - + CLIP_ACT=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 - R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. - + R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. + READ1_MAX_BASES_TO_WRITE=Integer - R1_MAX_BASES=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. - + R1_MAX_BASES=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 - R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. - + R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. + READ2_MAX_BASES_TO_WRITE=Integer - R2_MAX_BASES=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. - + R2_MAX_BASES=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 + 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. - Possible values: {true, false} - + Possible values: {true, false} + @more_info@ </help>