comparison umi-tools_extract.xml @ 19:7a7e33d28f62 draft default tip

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

18:015cf18f4a15

<tool id="umi_tools_extract" name="UMI-tools extract" 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" />
    <command detect_errors="exit_code"><![CDATA[
    @COMMAND_LINK@

    umi_tools extract

            </when>
        </conditional>
        <expand macro="log_input_macro"/>
    </inputs>
    <outputs>
        <data name="out" format_source="input_read1" label="${tool.name} on ${on_string}: Reads" >
            <filter>input_type_cond['input_type'] in ['single', 'paired']</filter>
        </data>
        <data name="out2" format_source="input_read2" label="${tool.name} on ${on_string}: Reads2" >
            <filter>input_type_cond['input_type'] == 'paired'</filter>
        </data>
        <collection name="out_paired_collection" type="paired" label="${tool.name} on ${on_string}: Reads">
            <data name="forward" format_source="input_readpair" />
            <data name="reverse" format_source="input_readpair" />

            <conditional name="extract_method_cond">
                <param name="prime3" value="true" />
            </conditional>
            <param name="quality_selector" value="true" />
            <param name="quality_filter_threshold" value="10" />
            <param name="quality_encoding" value="phred33" />
            <param name="log" value="true"/>
            <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
            <output name="out_log" >
                <assert_contents>
                    <has_text text="Input Reads: 100" />

19:7a7e33d28f62

<tool id="umi_tools_extract" name="UMI-tools extract" 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" />
    <command detect_errors="exit_code"><![CDATA[
    @COMMAND_LINK@

    umi_tools extract

            </when>
        </conditional>
        <expand macro="log_input_macro"/>
    </inputs>
    <outputs>
        <data name="out" format_source="input_read1" label="${tool.name} on ${on_string}: Forward reads" >
            <filter>input_type_cond['input_type'] in ['single', 'paired']</filter>
        </data>
        <data name="out2" format_source="input_read2" label="${tool.name} on ${on_string}: Reverse reads" >
            <filter>input_type_cond['input_type'] == 'paired'</filter>
        </data>
        <collection name="out_paired_collection" type="paired" label="${tool.name} on ${on_string}: Reads">
            <data name="forward" format_source="input_readpair" />
            <data name="reverse" format_source="input_readpair" />

            <conditional name="extract_method_cond">
                <param name="prime3" value="true" />
            </conditional>
            <param name="quality_selector" value="true" />
            <param name="quality_filter_threshold" value="10" />
            <param name="log" value="true"/>
            <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
            <output name="out_log" >
                <assert_contents>
                    <has_text text="Input Reads: 100" />