comparison samtools_fastx.xml @ 2:720217c23995 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

1:a8d69aee190e

<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy1">
    <description>extract FASTA or FASTQ from alignment files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio"/>
    <expand macro="version_command" />
    <command><![CDATA[
@ADDTHREADS@ 
## name sort input file if neccessary
#if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
    samtools sort -@ \$addthreads -n '$input' > input &&
#else:
    ln -s '$input' input &&
#end if

#set command=str($output_fmt_cond.output_fmt_select)[:5]

    -1 forward.$output_fmt_cond.output_fmt_select
#end if
#if 'r2' in str($outputs):
    -2 reverse.$output_fmt_cond.output_fmt_select
#end if
#if str($inclusive_filter) != 'None':
    #set $filter = $inclusive_filter
    @FLAGS@
    -f $flags
#end if
#if str($exclusive_filter) != 'None':
    #set $filter = $exclusive_filter
    @FLAGS@
    -F $flags
#end if
#if str($exclusive_filter) != 'None':
    #set $filter = $exclusive_filter_all
    @FLAGS@
    -G $flags
#end if
#if 's' in str($outputs):
    -s singletons.$output_fmt_cond.output_fmt_select
#end if
#if str($idxout_cond.idxout_select) == 'yes':
    #if str($idxout_cond.write1st) == 'yes':

    #if str($idxout_cond.quality_tag) != '':
        --quality-tag $idxout_cond.quality_tag
    #end if
#end if

input 

#if str($outputs)=='None' or 'other' in str($outputs):
    ## since currently stdout in not zipped (samtools doesn't know about the extension)
    #if str($output_fmt_cond.output_fmt_select).endswith('.gz'):
        | gzip - 
    #end if
    > output.$output_fmt_cond.output_fmt_select
    && ln -s output.$output_fmt_cond.output_fmt_select output
#else
    ## otherwise the remaining sequences would show up in the datasets info box

            <option value="" selected="True">no</option>
            <option value="-n">Do not append /1 and /2 to read names</option>
            <option value="-N">always append /1 and /2 to read name</option>
        </param>
        <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
            <expand macro="flag_options" />
        </param>
        <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
            <expand macro="flag_options" />
        </param>
        <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
            <expand macro="flag_options" />
        </param>

            <param name="outputs" value="r0,r1,r2" />
            <output name="nonspecific" file="samtools_fastx-out3-1.fasta" ftype="fasta" />
            <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" />
            <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"  compare="sim_size" />
        </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" />
            <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" />
            <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" />
        </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="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" />
            <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" />
            <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" />
        </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>

            <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" />
            <param name="copy_tags" value="-t" />
            <param name="copy_arb_tags" value="MD,ia" />
            <param name="read_numbering" value="-N"/>
            <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />
            <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />
            <output name="singletons" file="7.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>

2:720217c23995

<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>extract FASTA or FASTQ from alignment files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio"/>
    <expand macro="version_command" />
    <command><![CDATA[
@ADDTHREADS@
## name sort input file if neccessary
#if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
    samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
#else:
    ln -s '$input' input &&
#end if

#set command=str($output_fmt_cond.output_fmt_select)[:5]

    -1 forward.$output_fmt_cond.output_fmt_select
#end if
#if 'r2' in str($outputs):
    -2 reverse.$output_fmt_cond.output_fmt_select
#end if
#set $filter = $inclusive_filter
@FLAGS@
-f $flags
#set $filter = $exclusive_filter
@FLAGS@
-F $flags
#set $filter = $exclusive_filter_all
@FLAGS@
-G $flags
#if 's' in str($outputs):
    -s singletons.$output_fmt_cond.output_fmt_select
#end if
#if str($idxout_cond.idxout_select) == 'yes':
    #if str($idxout_cond.write1st) == 'yes':

    #if str($idxout_cond.quality_tag) != '':
        --quality-tag $idxout_cond.quality_tag
    #end if
#end if

input

#if str($outputs)=='None' or 'other' in str($outputs):
    ## since currently stdout in not zipped (samtools doesn't know about the extension)
    #if str($output_fmt_cond.output_fmt_select).endswith('.gz'):
        | gzip -
    #end if
    > output.$output_fmt_cond.output_fmt_select
    && ln -s output.$output_fmt_cond.output_fmt_select output
#else
    ## otherwise the remaining sequences would show up in the datasets info box

            <option value="" selected="True">no</option>
            <option value="-n">Do not append /1 and /2 to read names</option>
            <option value="-N">always append /1 and /2 to read name</option>
        </param>
        <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
            <expand macro="flag_options"/>
        </param>
        <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
            <expand macro="flag_options" s256="true" s2048="true"/>
        </param>
        <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
            <expand macro="flag_options" />
        </param>

            <param name="outputs" value="r0,r1,r2" />
            <output name="nonspecific" file="samtools_fastx-out3-1.fasta" ftype="fasta" />
            <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" />
            <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="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" decompress="true" />
            <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" decompress="true" />
            <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>

            <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="index_format" value="n2i2"/>
            </conditional>
            <param name="copy_tags" value="-t" />
            <param name="copy_arb_tags" value="MD,ia" />
            <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>