comparison bealign.xml @ 8:8a7462c0ac14 draft default tip

planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988

7:a07a2d9ddd42

<?xml version="1.0"?>
<tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>to a reference using a codon alignment algorithm</description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="5.1.0">gawk</requirement>
        <requirement type="package" version="1.14">samtools</requirement>
    </expand>
    <version_command>bealign --version</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
    ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might

            <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
                <option value="codon" selected="True">Codon</option>
                <option value="dna">DNA</option>
                <option value="amino">Amino acids</option>
            </param>
            <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix">
                <option value="BLOSUM62" selected="True">Blocks substitution</option>
                <option value="DNA65">DNA, 65% expected identity</option>
                <option value="DNA70">DNA, 70% expected identity</option>
                <option value="DNA88">DNA, 88% expected identity</option>
                <option value="DNA80">DNA, 80% expected identity</option>

                <option value="PAM200">PAM 200 substitution</option>
                <option value="PAM250">PAM 250 substitution</option>
                <option value="HIV_BETWEEN_F">HIV between+F</option>
            </param>
            <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
            <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
            <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
        </section>
    </inputs>
    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${on_string} - Aligned Sequences" />
        <data name="background" format="bam" label="${tool.name} on ${on_string} - Background" >
            <filter>background_source['sequences']</filter>
        </data>
        <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" >
            <filter>select_reference['save_reference']</filter>
        </data>
        <data name="discarded_reads" format="fasta">
            <filter>advanced['discard']</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="fasta" value="query.fa" />
            <param name="reference_type" value="dataset" />
            <param name="score_matrix" value="HIV_BETWEEN_F" />
            <param name="reference" ftype="fasta" value="reference.fa" />
            <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />
        </test>
        <test>
            <param name="input" ftype="fasta" value="query.fa" />
            <param name="reference_type" value="preset" />
            <param name="reference" value="CoV2-nsp8" />
            <param name="score_matrix" value="HIV_BETWEEN_F" />
            <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/>

8:8a7462c0ac14

<tool id="bioext_bealign" name="Align sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>to a reference using a codon alignment algorithm</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="5.3.0">gawk</requirement>
        <requirement type="package" version="1.19.2">samtools</requirement>
    </expand>
    <version_command>bealign --version</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
    ## Some downstream tools, such as the TN-93 clustering tool and RAxML, might

            <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
                <option value="codon" selected="True">Codon</option>
                <option value="dna">DNA</option>
                <option value="amino">Amino acids</option>
            </param>
            <param argument="--score-matrix" type="select" label="Parametrize using score matrix">
                <option value="BLOSUM62" selected="True">Blocks substitution</option>
                <option value="DNA65">DNA, 65% expected identity</option>
                <option value="DNA70">DNA, 70% expected identity</option>
                <option value="DNA88">DNA, 88% expected identity</option>
                <option value="DNA80">DNA, 80% expected identity</option>

                <option value="PAM200">PAM 200 substitution</option>
                <option value="PAM250">PAM 250 substitution</option>
                <option value="HIV_BETWEEN_F">HIV between+F</option>
            </param>
            <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" />
            <param argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" />
            <param argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" />
        </section>
    </inputs>
    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${on_string} - Aligned Sequences" />
        <data name="background" format="bam" label="${tool.name} on ${on_string} - Background" >
            <filter>background_source['sequences']</filter>
        </data>
        <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" >
            <filter>select_reference['reference_type'] == 'preset' and select_reference['save_reference']</filter>
        </data>
        <data name="discarded_reads" format="fasta">
            <filter>advanced['discard']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" ftype="fasta" value="query.fa" />
            <param name="reference_type" value="dataset" />
            <param name="score_matrix" value="HIV_BETWEEN_F" />
            <param name="reference" ftype="fasta" value="reference.fa" />
            <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />
        </test>
        <test expect_num_outputs="1">
            <param name="input" ftype="fasta" value="query.fa" />
            <param name="reference_type" value="preset" />
            <param name="reference" value="CoV2-nsp8" />
            <param name="score_matrix" value="HIV_BETWEEN_F" />
            <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/>