Mercurial > repos > devteam > picard
diff picard_SamToFastq.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_SamToFastq.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_SamToFastq.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,156 +1,143 @@ -<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> +<tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">3</token> + <token name="@WRAPPER_VERSION@">0</token> </macros> <xrefs> <xref type="bio.tools">picard_samtofastq</xref> </xrefs> - <expand macro="requirements" /> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ - picard - SamToFastq + picard SamToFastq - INPUT='$escaped_element_identifier' + --INPUT '$escaped_element_identifier' #if str($single_or_paired) == "pe_interleaved": - FASTQ='${interleaved_fastq}' - INTERLEAVE=TRUE + --FASTQ '${interleaved_fastq}' + --INTERLEAVE TRUE #else if str($single_or_paired) == "pe_sep": - F='${fq1}' - F2='${fq2}' - FU='${fq_u}' + --F '${fq1}' + --F2 '${fq2}' + --FU '${fq_u}' #else - F='${fq_single}' + --F '${fq_single}' #end if - RE_REVERSE="${re_reverse}" + --RE_REVERSE '${re_reverse}' - INCLUDE_NON_PF_READS="${include_non_pf_reads}" + -INCLUDE_NON_PF_READS '${include_non_pf_reads}' #if len(str($clipping_attribute)) > 0: - CLIPPING_ATTRIBUTE="${clipping_attribute}" + --CLIPPING_ATTRIBUTE '${clipping_attribute}' #end if #if len(str($clipping_action)) > 0: - CLIPPING_ACTION="${clipping_action}" + --CLIPPING_ACTION '${clipping_action}' #end if - READ1_TRIM="${read1_trim}" + --READ1_TRIM '${read1_trim}' #if int($read1_max_bases_to_write) > -1: - READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" + --READ1_MAX_BASES_TO_WRITE '${read1_max_bases_to_write}' #end if - READ2_TRIM="${read2_trim}" + --READ2_TRIM '${read2_trim}' #if int($read2_max_bases_to_write) > -1: - READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}" + --READ2_MAX_BASES_TO_WRITE '${read2_max_bases_to_write}' #end if - INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" + --INCLUDE_NON_PRIMARY_ALIGNMENTS '${include_non_primary_alignments}' - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR + --VALIDATION_STRINGENCY '${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="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 expect_num_outputs="5"> - <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> - <param name="single_or_paired" value="pe_interleaved" /> - <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 expect_num_outputs="5"> - <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> - <param name="single_or_paired" value="pe_sep" /> - <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 expect_num_outputs="5"> - <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/> - <param name="single_or_paired" value="se" /> - <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> + <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 expect_num_outputs="5"> + <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> + <param name="single_or_paired" value="pe_interleaved"/> + <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 expect_num_outputs="5"> + <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> + <param name="single_or_paired" value="pe_sep"/> + <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 expect_num_outputs="5"> + <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/> + <param name="single_or_paired" value="se"/> + <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** @@ -223,5 +210,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>