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view picard_SamToFastq.xml @ 26:fc3866ddc7b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author | iuc |
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date | Mon, 22 Aug 2022 09:54:37 +0000 |
parents | e65f2d5fd3d8 |
children | fdca9493e09b |
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<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> <macros> <import>picard_macros.xml</import> <token name="@WRAPPER_VERSION@">2</token> </macros> <xrefs> <xref type="bio.tools">picard_samtofastq</xref> </xrefs> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ picard SamToFastq INPUT='$escaped_element_identifier' #if str($single_or_paired) == "pe_interleaved": FASTQ='${interleaved_fastq}' INTERLEAVE=TRUE #else if str($single_or_paired) == "pe_sep": F='${fq1}' F2='${fq2}' FU='${fq_u}' #else F='${fq_single}' #end if RE_REVERSE="${re_reverse}" INCLUDE_NON_PF_READS="${include_non_pf_reads}" #if len(str($clipping_attribute)) > 0: CLIPPING_ATTRIBUTE="${clipping_attribute}" #end if #if len(str($clipping_action)) > 0: CLIPPING_ACTION="${clipping_action}" #end if 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 @TMPDIR_OPTION@ ]]></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="single_or_paired" type="select" label="Output format"> <option value="se" >Single-end</option> <option value="pe_interleaved" selected="true">Paired-end (one interleaved output file)</option> <option value="pe_sep">Paired-end (two separate output files)</option> </param> <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"/> <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads; default=False"/> <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/> <param name="clipping_action" type="text" value="" label="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" help="CLIPPING_ACTION; default=null"/> <param name="read1_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 1" help="READ1_TRIM; default=0"/> <param name="read1_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 1 after trimming" help="READ1_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="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> <outputs> <data format="fastqsanger" name="fq_single" label="${tool.name} on ${on_string}: reads as fastq"> <filter>output_type['single_or_paired'] == 'se'</filter> </data> <data format="fastqsanger" name="interleaved_fastq" label="Interleaved pairs from ${tool.name} on ${on_string}"> <filter>output_type['single_or_paired'] == 'pe_interleaved'</filter> </data> <data format="fastqsanger" name="fq1" label="Paired-end forward strand from ${tool.name} on ${on_string}"> <filter>output_type['single_or_paired'] == 'pe_sep'</filter> </data> <data format="fastqsanger" name="fq2" label="Paired-end reverse strand from ${tool.name} on ${on_string}"> <filter>output_type['single_or_paired'] == 'pe_sep'</filter> </data> <data format="fastqsanger" name="fq_u" label="Paired-end unpaired reads from ${tool.name} on ${on_string}"> <filter>output_type['single_or_paired'] == 'pe_sep'</filter> </data> </outputs> <tests> <test> <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> <param name="single_or_paired" value="pe_interleaved" /> <param name="output_per_rg" value="false"/> <param name="re_reverse" value="true"/> <param name="include_non_pf_reads" value="false"/> <param name="clipping_attribute" value="" /> <param name="clipping_action" value="" /> <param name="read1_trim" value="0" /> <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"/> <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/> </test> <test> <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> <param name="single_or_paired" value="pe_sep" /> <param name="output_per_rg" value="false"/> <param name="re_reverse" value="true"/> <param name="include_non_pf_reads" value="false"/> <param name="clipping_attribute" value="" /> <param name="clipping_action" value="" /> <param name="read1_trim" value="0" /> <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"/> <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/> <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/> <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/> </test> <test> <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/> <param name="single_or_paired" value="se" /> <param name="output_per_rg" value="false"/> <param name="re_reverse" value="true"/> <param name="include_non_pf_reads" value="false"/> <param name="clipping_attribute" value="" /> <param name="clipping_action" value="" /> <param name="read1_trim" value="0" /> <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"/> <output name="fq_single" file="picard_SamToFastq_se.fq" ftype="fastqsanger"/> </test> </tests> <help> **Purpose** Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset 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. ----- .. class:: warningmark **DANGER: Multiple Outputs** Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing! @dataset_collections@ @description@ FASTQ=File 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. 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 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 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. 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} 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} 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} CLIPPING_ATTRIBUTE=String 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. READ1_TRIM=Integer 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. READ2_TRIM=Integer 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. 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. Possible values: {true, false} @more_info@ </help> <expand macro="citations" /> </tool>