comparison umi-tools_group.xml @ 17:428735be9764 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a

16:257be15474a7

<tool id="umi_tools_group" name="UMI-tools group" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Extract UMI from fastq files</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.21">samtools</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
        @LINK_SAM_BAM_INPUT@

            @SAMBAM_OPTIONS@
            @FULLSC_OPTIONS@
            -I '$input_file' -S grouped.bam
            @ADVANCED_OPTIONS@
            @LOG@
            ## TODO using samtools sort is a workaround, for the following error that appears when Galaxy
            ## compares the generated file with the one in test-data
            ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
            ## may be dropped in the future
            --no-sort-output
            && samtools sort --no-PG grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM

        <expand macro="fullsc_options_macro"/>
        <expand macro="advanced_options_macro"/>
        <expand macro="log_input_macro"/>
    </inputs>
    <outputs>
        <data format="bam" name="output" />
        <data format="tabular" name="group_out">
            <filter>group_output</filter>
        </data>
        <expand macro="log_output_macro"/>
    </outputs>
    <tests>

17:428735be9764

<tool id="umi_tools_group" name="UMI-tools group" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Extract UMI from fastq files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements">
        <requirement type="package" version="1.21">samtools</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
        @LINK_SAM_BAM_INPUT@

            @SAMBAM_OPTIONS@
            @FULLSC_OPTIONS@
            -I '$input_file' -S grouped.bam
            @ADVANCED_OPTIONS@
            @LOG@
            ## using samtools sort is a workaround, for the following error that appears when Galaxy
            ## compares the generated file with the one in test-data
            ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
            ## may be dropped in the future
            --no-sort-output
            && samtools sort --no-PG grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM

        <expand macro="fullsc_options_macro"/>
        <expand macro="advanced_options_macro"/>
        <expand macro="log_input_macro"/>
    </inputs>
    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string}: Tagged BAM"/>
        <data format="tabular" name="group_out" label="${tool.name} on ${on_string}: Read groups">
            <filter>group_output</filter>
        </data>
        <expand macro="log_output_macro"/>
    </outputs>
    <tests>