comparison picard_SamToFastq.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

32:f9242e01365a

<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@">3</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

  ]]></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>

**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.

                                Possible values: {true, false}

@more_info@

  </help>
  <expand macro="citations" />
</tool>

33:3f254c5ced1d

<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@">0</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

  ]]></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>

**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.

                                Possible values: {true, false}

@more_info@

  </help>
    <expand macro="citations"/>
</tool>