comparison samtools_fastx.xml @ 4:66e23b11feae draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a

3:b3d99709fe1a

<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>extract FASTA or FASTQ from alignment files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

            </param>
            <when value="no" />
	    <when value="yes">
                <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" />
                <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" />
                <param name="index_format" argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
                    <help>
The index-format string describes how to parse the barcode and quality tags, for example:
   i14i8       the first 14 characters are index 1, the next 8 characters are index 2
   n8i14       ignore the first 8 characters, and use the next 14 characters for index 1
   If the tag contains a separator, then the numeric part can be replaced with '*' to mean
   'read until the separator or end of tag', for example:
   n*i*        ignore the left part of the tag until the separator, then use the second part
               of the tag as index 1
                    </help>
                </param>
                <param name="barcode_tag" argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
                <param name="quality_tag" argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)">

            </actions>
        </data>
    </outputs>
    <tests>
        <!-- tests from original Galaxy tool -->
        <test>
            <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta" />
            </conditional>
            <param name="outputs" value="other" />
            <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" />
        </test>
        <test>
            <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />
            <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" />
            <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" />
            <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />

            <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" />
        </test>
        <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used
             for compressing stdout does not give exactly the same file contents .. the other
             compressed files seem to)-->
        <test>
            <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta.gz" />
            </conditional>
            <param name="outputs" value="other" />
            <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/>
        </test>
        <test>
            <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger.gz" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />
            <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
        </test>
        <test>
            <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta.gz" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />

            <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" />
        </test>
        <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313-->
        <!--# basic 2 output test without singleton tracking-->
        <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
        <test>
            <param name="input" value="bam2fq.001.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,other" />

            <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="1.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# basic 2 output test with singleton tracking but no singleton-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
        <test>
            <param name="input" value="bam2fq.001.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" />
            <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# basic 2 output test with singleton tracking with a singleton in the middle-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");-->
        <test>
            <param name="input" value="bam2fq.002.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="3.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# basic 2 output test with singleton tracking with a singleton as last read-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");-->
        <test>
            <param name="input" value="bam2fq.003.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="4.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# tag output test with singleton tracking with a singleton as last read-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
        <test>
            <param name="input" value="bam2fq.004.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="yes"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="4.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# test -O flag with no OQ tags-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
        <test>
            <param name="input" value="bam2fq.010.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="output_quality" value="-O" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="yes"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc10.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# test -O flag with OQ tags-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");-->
        <test>
            <param name="input" value="bam2fq.010.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="output_quality" value="-O" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="yes"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc10.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# tag output test with separators and -N flag-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test>
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <param name="read_numbering" value="-N"/>
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="yes"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n*i*"/>
            </conditional>
            <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc_split.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# -t flag-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test>
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="6.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# -T flag-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test>
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# -i flag with no index-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test>
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="ilumina_casava" value="-i" />
            </conditional>

            <param name="read_numbering" value="-N"/>
            <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" />
            <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# -i flag with index-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
        <test>
            <param name="input" value="bam2fq.004.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="ilumina_casava" value="-i" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="yes"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" />
            <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="8.i.fq.expected" ftype="fastqsanger" />
        </test>
    </tests>
    <help><![CDATA[
This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a
SAM or BAM file in FASTA or FASTQ format.

4:66e23b11feae

<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>extract FASTA or FASTQ from alignment files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

            </param>
            <when value="no" />
	    <when value="yes">
                <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" />
                <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" />
                <param argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
                    <help>
The index-format string describes how to parse the barcode and quality tags, for example:
   i14i8       the first 14 characters are index 1, the next 8 characters are index 2
   n8i14       ignore the first 8 characters, and use the next 14 characters for index 1
   If the tag contains a separator, then the numeric part can be replaced with '*' to mean
   'read until the separator or end of tag', for example:
   n*i*        ignore the left part of the tag until the separator, then use the second part
               of the tag as index 1
                    </help>
                </param>
                <param argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
                <param argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)">

            </actions>
        </data>
    </outputs>
    <tests>
        <!-- tests from original Galaxy tool -->
        <test expect_num_outputs="1">
            <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta" />
            </conditional>
            <param name="outputs" value="other" />
            <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" />
        </test>
        <test expect_num_outputs="3">
            <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />
            <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" />
            <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" />
            <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" />
        </test>
        <test expect_num_outputs="3">
            <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />

            <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" />
        </test>
        <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used
             for compressing stdout does not give exactly the same file contents .. the other
             compressed files seem to)-->
        <test expect_num_outputs="1">
            <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta.gz" />
            </conditional>
            <param name="outputs" value="other" />
            <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/>
        </test>
        <test expect_num_outputs="3">
            <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger.gz" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />
            <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
            <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
        </test>
        <test expect_num_outputs="3">
            <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fasta.gz" />
            </conditional>
            <param name="outputs" value="r0,r1,r2" />

            <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" />
        </test>
        <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313-->
        <!--# basic 2 output test without singleton tracking-->
        <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
        <test expect_num_outputs="3">
            <param name="input" value="bam2fq.001.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,other" />

            <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="1.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# basic 2 output test with singleton tracking but no singleton-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
        <test expect_num_outputs="4">
            <param name="input" value="bam2fq.001.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" />
            <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# basic 2 output test with singleton tracking with a singleton in the middle-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");-->
        <test expect_num_outputs="4">
            <param name="input" value="bam2fq.002.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="3.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# basic 2 output test with singleton tracking with a singleton as last read-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");-->
        <test expect_num_outputs="4">
            <param name="input" value="bam2fq.003.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="4.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# tag output test with singleton tracking with a singleton as last read-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
        <test expect_num_outputs="5">
            <param name="input" value="bam2fq.004.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="true"/>
                <param name="write2nd" value="false"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="4.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# test -O flag with no OQ tags-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
        <test expect_num_outputs="5">
            <param name="input" value="bam2fq.010.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="output_quality" value="-O" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="true"/>
                <param name="write2nd" value="false"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc10.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# test -O flag with OQ tags-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");-->
        <test expect_num_outputs="5">
            <param name="input" value="bam2fq.010.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="output_quality" value="-O" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="true"/>
                <param name="write2nd" value="false"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc10.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# tag output test with separators and -N flag-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test expect_num_outputs="5">
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <param name="read_numbering" value="-N"/>
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="true"/>
                <param name="write2nd" value="false"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n*i*"/>
            </conditional>
            <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" />

            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="bc_split.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# -t flag-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test expect_num_outputs="4">
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="6.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# -T flag-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test expect_num_outputs="4">
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />

            <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
        </test>
        <!--# -i flag with no index-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
        <test expect_num_outputs="6">
            <param name="input" value="bam2fq.005.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="ilumina_casava" value="-i" />
            </conditional>

            <param name="read_numbering" value="-N"/>
            <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" />
            <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="11.i.fq.expected" ftype="fastqsanger" />
            <output name="i2"  file="11.i2.fq.expected" ftype="fastqsanger" />
        </test>
        <!--# -i flag with index-->
        <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
        <test expect_num_outputs="6">
            <param name="input" value="bam2fq.004.sam" ftype="sam" />
            <conditional name="output_fmt_cond">
                <param name="output_fmt_select" value="fastqsanger" />
                <param name="ilumina_casava" value="-i" />
            </conditional>
            <param name="outputs" value="r1,r2,s,other" />
            <conditional name="idxout_cond">
                <param name="idxout_select" value="yes"/>
                <param name="write1st" value="true"/>
                <param name="barcode_tag" value="BC"/>
                <param name="index_format" value="n2i2"/>
            </conditional>
            <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" />
            <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />
            <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
            <output name="i1"  file="8.i.fq.expected" ftype="fastqsanger" />
            <output name="i2"  file="8.i2.fq.expected" ftype="fastqsanger" />
        </test>
    </tests>
    <help><![CDATA[
This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a
SAM or BAM file in FASTA or FASTQ format.