comparison umi-tools_extract.xml @ 8:3cfd8e1073d7 draft

planemo upload commit f6178c9e071a2158a35b82a3607f6dc8a767675c

7:4756f7765416

<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1">
    <description>Extract UMI from fastq files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    @COMMAND_LINK@

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out" format_source="input_single">
            <filter>input_type['type'] == "single"</filter>
        </data>
        <data name="out1" format_source="input_read1">
            <filter>input_type['type'] !== "single"</filter>
        </data>
        <data name="out2" format_source="input_read2">
            <filter>input_type['type'] !== "single"</filter>
        </data>
        <data name="out_log" format="txt">
            <filter>print_log == True</filter>
        </data>
    </outputs>
    <tests>

            <param name="bc_pattern" value="XXXNNN" />
            <param name="prime3" value="0" />
            <param name="quality_selector" value="true" />
            <param name="quality_filter_threshold" value="10" />
            <param name="quality_encoding" value="phred33" />
            <output name="out" file="out_SE.fastq" />
            <output name="out_log" file="out_single.log" lines_diff="22"/>
        </test>
        <test>
            <param name="type" value="paired" />
            <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
            <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
            <param name="bc_pattern" value="NNNXXX" />
            <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
            <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
            <output name="out_log" file="out_paired.log" lines_diff="16"/>
        </test>
        <test>
            <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed -->
            <param name="input_readpair" >
                <collection type="paired">
                    <element name="forward" ftype="fastq" value="t_R1.fastq" />
                    <element name="reverse" ftype="fastq" value="t_R2.fastq" />
                </collection>
            </param>
            <param name="bc_pattern" value="NNNXXX" />
            <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
            <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
            <output name="out_log" file="out_paired.log" lines_diff="25" />
        </test>
        <test>
            <param name="type" value="paired" />
            <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
            <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
            <param name="extract_method" value="string" />
            <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" />
            <param name="use_barcodes" value="yes" />
            <param name="filter_barcode_file" value="scrb_seq_barcodes" />
            <output name="out2" file="scrb_extract.fastq.gz" decompress="true" />
        </test>
        <test><!-- same as above but with regex barcode-->
            <param name="type" value="paired" />
            <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
            <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
            <param name="extract_method" value="regex" />
            <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" />
            <param name="use_barcodes" value="yes" />
            <param name="filter_barcode_file" value="scrb_seq_barcodes" />
            <output name="out2" file="scrb_extract.fastq.gz" decompress="true" />
        </test>
    </tests>
    <help><![CDATA[

8:3cfd8e1073d7

<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.2">
    <description>Extract UMI from fastq files</description>
    <macros>
        <import>macros.xml</import>
        <macro name="out_conditional">
            <actions>
                <conditional name="input_type.type">
                    <when value="paired_collection" >
                        <action type="format">
                            <option type="from_param" name="input_type.input_readpair" param_attribute="forward.ext" />
                        </action>
                    </when>
                    <when value="paired" >
                        <action type="format">
                            <option type="from_param" name="input_type.input_read1"  param_attribute="ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </macro>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    @COMMAND_LINK@

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out" format_source="input_single" label="Reads: ${tool.name} on ${on_string}" >
            <filter>input_type['type'] == "single"</filter>
        </data>
        <data name="out1" format_source="input_read1" label="Reads1: ${tool.name} on ${on_string}" >
            <filter>input_type['type'] != "single"</filter>
            <expand macro="out_conditional" />
        </data>
        <data name="out2" format_source="input_read2" label="Reads2: ${tool.name} on ${on_string}" >
            <filter>input_type['type'] != "single"</filter>
            <expand macro="out_conditional" />
        </data>
        
        <data name="out_log" format="txt">
            <filter>print_log == True</filter>
        </data>
    </outputs>
    <tests>

            <param name="bc_pattern" value="XXXNNN" />
            <param name="prime3" value="0" />
            <param name="quality_selector" value="true" />
            <param name="quality_filter_threshold" value="10" />
            <param name="quality_encoding" value="phred33" />
            <output name="out" file="out_SE.fastq" ftype="fastq" />
            <output name="out_log" >
                <assert_contents>
                    <has_text text="Input Reads: 100" />
                    <has_text text="umi quality: 28" />
                    <has_text text="Reads output: 72" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type" value="paired" />
            <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
            <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
            <param name="bc_pattern" value="NNNXXX" />
            <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" />
            <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" />
            <output name="out_log" >
                <assert_contents>
                    <has_text text="Input Reads: 100" />
                    <has_text text="Reads output: 100" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed -->
            <param name="paired_type" value="no" />
            <param name="input_readpair" >
                <collection type="paired" >
                    <element name="forward" ftype="fastq" value="t_R1.fastq" />
                    <element name="reverse" ftype="fastq" value="t_R2.fastq" />
                </collection>
            </param>
            <param name="bc_pattern" value="NNNXXX" />
            <output name="out1" file="out_R1.fastq" ftype="fastq" />
            <output name="out2" file="out_R2.fastq" ftype="fastq" />
            <output name="out_log" >
                <assert_contents>
                    <has_text text="Input Reads: 100" />
                    <has_text text="Reads output: 100" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type" value="paired" />
            <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
            <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
            <param name="extract_method" value="string" />
            <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" />
            <param name="use_barcodes" value="yes" />
            <param name="filter_barcode_file" value="scrb_seq_barcodes" />
            <output name="out2" file="scrb_extract.fastq.gz" decompress="true"  ftype="fastq.gz" />
        </test>
        <test><!-- same as above but with regex barcode-->
            <param name="type" value="paired" />
            <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
            <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
            <param name="extract_method" value="regex" />
            <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" />
            <param name="use_barcodes" value="yes" />
            <param name="filter_barcode_file" value="scrb_seq_barcodes" />
            <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" />
        </test>
        <test><!-- CelSeq2 example -->
            <param name="type" value="paired" />
            <param name="input_read1" value="read_R1.200.gz" ftype="fastq.gz" />
            <param name="input_read2" value="read_R2.200.gz" ftype="fastq.gz" />
            <param name="extract_method" value="string" />
            <param name="bc_pattern" value="NNNNNNCCCCCC" />
            <output name="out1" file="read_R1.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" />
            <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" />
        </test>
    </tests>
    <help><![CDATA[