comparison snipit.xml @ 2:92b9fd5f1f9f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 58fa50696846c7f6a5bcfc22a59243c80107e41a

1:9f23fe0cb70b

<tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">
    <description>Summarise snps relative to a reference sequence</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.7</token>
        <xml name="handle_background" tokens="format">
            <when value="@FORMAT@">
                <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" />
            </when>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">snipit</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        MPLCONFIGDIR=.matplotlib snipit '$alignment'
            #if str($ref.select) == 'by_id'
                -r '$ref.id'
            #end if
            #if str($style.labels.choose)
                -l '$style.labels.source'

            #if $dims.width > 0
                --width $dims.width
            #end if
            $dims.size_option
            $style.flip_vertical
            #if len($pos_restrict.include_positions)
                --include-positions
                #for $p in $pos_restrict.include_positions
                    '$p.pos'
                #end for

                --recombi-mode --recombi-references '$style.colouring.parent1,$style.colouring.parent2'
            #else
                -c $style.colouring.palette
            #end if
    ]]></command>
    <inputs>
        <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" />
        <conditional name="ref">
            <param name="select" type="select" label="The reference sequence ...">
                <option value="first">is the first sequence in the input</option>
                <option value="by_id">should be picked via its ID</option>
            </param>
            <when value="first" />
            <when value="by_id">

            <param argument="--size-option" type="select" value="scale" label="Plot sizing options">
                <option value="--size-option expand">expand</option>
                <option value="" selected="true">scale</option>
            </param>
        </section>
        <param argument="--write-snps" type="boolean" truevalue="-s" falsevalue="" label="Write out SNPs?" help="Produces extra CSV output with lists of SNPs per sequence in the alignment if enabled." />
    </inputs>
    <outputs>
        <data name="snp_plot" format="png" label="snipit on ${on_string}: Plot" from_work_dir="snp_plot.*">
            <change_format>

                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="alignment" value="input.fasta" />
            <section name="style">
                <conditional name="colouring">
                    <param name="palette" value="" />
                    <param name="parent1" value="USA_1" />
                    <param name="parent2" value="USA_5" />

2:92b9fd5f1f9f

<tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">
    <description>Summarise snps relative to a reference sequence</description>
    <macros>
        <token name="@TOOL_VERSION@">1.2</token>
        <xml name="handle_background" tokens="format">
            <when value="@FORMAT@">
                <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" />
            </when>
        </xml>
    </macros>
    <xrefs>
        <xref type="bio.tools">snipit</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">snipit</requirement>
    </requirements>
    <version_command>snipit -v</version_command>
    <command detect_errors="exit_code"><![CDATA[
        snipit '$alignment'
            #if str($ref.select) == 'by_id'
                -r '$ref.id'
            #end if
            #if str($style.labels.choose)
                -l '$style.labels.source'

            #if $dims.width > 0
                --width $dims.width
            #end if
            $dims.size_option
            $style.flip_vertical
            $show_indels
            #if len($pos_restrict.include_positions)
                --include-positions
                #for $p in $pos_restrict.include_positions
                    '$p.pos'
                #end for

                --recombi-mode --recombi-references '$style.colouring.parent1,$style.colouring.parent2'
            #else
                -c $style.colouring.palette
            #end if
    ]]></command>
    <environment_variables>
        <environment_variable name="MPLCONFIGDIR">.matplotlib</environment_variable>
    </environment_variables>
    <inputs>
        <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" />
        <conditional name="ref">
            <param name="select" type="select" label="The reference sequence ..."
            help="Please note that you will HAVE to specify the reference explicitly via its ID if you choose the 'recombinant mutations colouring' scheme and in this case the reference can NOT be one of the recombinant parents.">
                <option value="first">is the first sequence in the input</option>
                <option value="by_id">should be picked via its ID</option>
            </param>
            <when value="first" />
            <when value="by_id">

            <param argument="--size-option" type="select" value="scale" label="Plot sizing options">
                <option value="--size-option expand">expand</option>
                <option value="" selected="true">scale</option>
            </param>
        </section>
        <param argument="--show-indels" type="boolean" truevalue="--show-indels" falsevalue="" label="Try to plot indels" help="This is newly introduced functionality for which you may encounter bugs still." />
        <param argument="--write-snps" type="boolean" truevalue="-s" falsevalue="" label="Write out SNPs?" help="Produces extra CSV output with lists of SNPs per sequence in the alignment if enabled." />
    </inputs>
    <outputs>
        <data name="snp_plot" format="png" label="snipit on ${on_string}: Plot" from_work_dir="snp_plot.*">
            <change_format>

                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="alignment" value="input.fasta" />
            <conditional name="ref">
                <param name="select" value="by_id" />
                <param name="id" value="reference" />
            </conditional>
            <section name="style">
                <conditional name="colouring">
                    <param name="palette" value="" />
                    <param name="parent1" value="USA_1" />
                    <param name="parent2" value="USA_5" />