comparison ivar_trim.xml @ 4:db536ad45f28 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"

3:5d6ed46cc101

<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy0">
    <description>Trim reads in aligned BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #if $primer.source == "history"
            ln -s '$primer.input_bed' bed.bed &&
        #else
            ln -s '$primer.cached_bed.fields.path' bed.bed &&
        #end if 
        ln -s '$input_bam' sorted.bam &&
        ivar trim
        -i sorted.bam
        -b bed.bed
        -m $min_len
        -q $min_qual

            <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
            <param name="input_bed" value="covid19/ARTIC-V1.bed" />
            <param name="inc_primers" value="true" />
            <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
        </test>
        <!-- #1: Zika data-->
        <test>
            <conditional name="primer">
                <param name="source" value="history" />
                <param name="input_bed" value="zika/db/zika_primers.bed" />

4:db536ad45f28

<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy1">
    <description>Trim reads in aligned BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.8.1">python</requirement>
    </expand>
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #if $primer.source == "history"
            cp '$primer.input_bed' bed.bed &&
        #else
            cp '$primer.cached_bed.fields.path' bed.bed &&
        #end if
        python '$__tool_directory__/sanitize_bed.py' bed.bed &&

        ln -s '$input_bam' sorted.bam &&
        ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&

        ivar trim
        -i sorted.bam
        -b bed.bed
        -m $min_len
        -q $min_qual

            <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
            <param name="input_bed" value="covid19/ARTIC-V1.bed" />
            <param name="inc_primers" value="true" />
            <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
        </test>
        <test>
            <!-- Test with primer bed file that needs to be sanitized -->
            <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
            <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" />
            <param name="inc_primers" value="true" />
            <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
        </test>
        <!-- #1: Zika data-->
        <test>
            <conditional name="primer">
                <param name="source" value="history" />
                <param name="input_bed" value="zika/db/zika_primers.bed" />