annotate seqtk_seq.xml @ 11:8511b6d85fc7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit c819f01ae147fb23a1e5e91cee3626b6a19b9e03

<?xml version="1.0"?>
<tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@+galaxy1" profile="22.05">
    <description>common transformation of FASTA/Q</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk seq -q $q
-X $X
#if $n:
    -n '$n'
#end if
-l $l
-Q $Q
-s $s
-f $f
#if $M:
    -M '$M'
#end if
-L $L
$c
#if $direction != 'forward'
    $direction
#end if
$A
$C
$N
$x1
$x2
#if $in_file.is_of_type('fastqillumina')
    -V
#end if
'$in_file'
@CONDITIONAL_GZIP_OUT@
    ]]></command>
    <configfiles>
        <configfile filename="outputs.json">
#if $A and $in_file.is_of_type('fasta.gz', 'fastq.gz')
    #set $ext = "fasta.gz"
#elif $A
    #set $ext = "fasta"
#else
    #set $ext = $in_file.ext
#end if
{"default": {"ext": "$ext"}}
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="in_faq"/>
        <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" />
        <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" />
        <param argument="-n" type="text" value="" label="Masked bases converted to CHAR; leave empty for lowercase masking" />
        <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" />
        <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" help="Only applied during comparison to quality thresholds for masking" />
        <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" />
        <param argument="-f" type="float" value="1" label="Sample fraction of sequences" />
        <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" />
        <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" />
        <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" />
        <param name="direction" type="select" optional="false" label="Output complement">
            <option value="forward" selected="true">Forward only (Default)</option>
            <option value="-r">Reverse only (-r)</option>
            <option value="-R">Forward and Reverse (-R)</option>
        </param>
        <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Force FASTA output (discard quality)" />
        <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" />
        <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
        <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
        <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
    </inputs>
    <outputs provided_metadata_file="outputs.json">
        <data name="default" format="auto" label="${tool.name} on ${on_string}" />
    </outputs>

    <tests>
        <!-- This is a sorry excuse for a test for a tool which does way more
             than it should, but upstream decided to put a TON of functionality
             into a single tool rather than using the single responsibility
             principle. -->
        <test expect_num_outputs="1">
            <param name="in_file" value="seqtk_seq.fa"/>
            <param name="direction" value="-r"/>
            <param name="n" value=""/>
            <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
        </test>
        <test expect_num_outputs="1">
            <param name="in_file" value="seqtk_seq.fa.gz" ftype="fasta.gz"/>
            <param name="direction" value="-r"/>
            <param name="n" value=""/>
            <output name="default" file="seqtk_seq_revcom.fa.gz" ftype="fasta.gz"/>
        </test>
        <test expect_num_outputs="1">
            <param name="in_file" value="seqtk_seq.fa"/>
            <param name="direction" value="-R"/>
            <param name="n" value=""/>
            <output name="default" file="seqtk_seq_revcom_forw.fa" ftype="fasta"/>
        </test>
        <test expect_num_outputs="1">
            <param name="in_file" value="seqtk_trimfq.fq" ftype="fastq"/>
            <param name="A" value="True" />
            <output name="default" file="seqtk_seq_A.fasta" ftype="fasta"/>
        </test>
        <test expect_num_outputs="1">
            <param name="in_file" value="seqtk_trimfq.fq.gz" ftype="fastq.gz"/>
            <param name="A" value="True" />
            <output name="default" file="seqtk_seq_A.fasta.gz" ftype="fasta.gz"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Various utilities for transforming FASTA/Q data

@ATTRIBUTION@
    ]]></help>
    <expand macro="citation" />
</tool>