comparison cutadapt.xml @ 27:de6cebe3c043 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"

26:44e2cc14f75b

cutadapt

-j=\${GALAXY_SLOTS:-4}

#if str( $library.type ) == "single":
    @read1_options@
    #if 'multiple_output' in $output_selector:
        --output='split/{name}.${input_1.ext}'
    #else:

'${read1}'
#if $paired:
    '${read2}'
#end if

#if 'report' in $output_selector:
    > report.txt
#end if

            <param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." />
        </section>

        <!-- Read Modification Options -->
        <section name="read_mod_options" title="Read Modification Options">
            <param argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
                <sanitizer>
                    <valid initial="string.digits"><add value="," /></valid>
                </sanitizer>
                <validator type="regex">[0-9,]+</validator>
            </param>

            <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option>
            <option value="too_short_file">Too short reads: write reads that are too short according to minimum length specified (default: discard reads).</option>
            <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option>
            <option value="untrimmed_file">Untrimmed reads: write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file (default: output to same file as trimmed)</option>
            <option value="multiple_output">Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)</option>
        </param>
    </inputs>

    <outputs>
        <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">

        <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
            <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
            <filter>output_selector and 'too_long_file' in output_selector</filter>
            <expand macro="inherit_format_2" />
        </data>

        <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs"  >
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
            <filter>output_selector and 'multiple_output' in output_selector</filter>
        </collection>
    </outputs>

            <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
            <assert_command>
                <has_text text="--discard-trimmed"/>
            </assert_command>
        </test>
        <!-- Ensure rest file output works -->
        <test expect_num_outputs="2">
            <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>

                    </conditional>
                </repeat>
            </section>
            <param name="output_filtering" value="default"/>
            <param name="read_modification" value="none"/>
            <param name="output_selector" value="rest_file"/>
            <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
            <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
        </test>
        <!-- Ensure nextseq-trim option works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />

            <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
            <assert_command>
                <has_text text="TGTAGGCCX"/>
            </assert_command>
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark

27:de6cebe3c043

cutadapt

-j=\${GALAXY_SLOTS:-4}

#if 'json_stats' in $output_selector:
        --json stats.json
#end if

#if str( $library.type ) == "single":
    @read1_options@
    #if 'multiple_output' in $output_selector:
        --output='split/{name}.${input_1.ext}'
    #else:

'${read1}'
#if $paired:
    '${read2}'
    #if $library.r2.quality_cutoff2:
        -Q=$library.r2.quality_cutoff2
    #end if
#end if

#if 'report' in $output_selector:
    > report.txt
#end if

            <param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." />
        </section>

        <!-- Read Modification Options -->
        <section name="read_mod_options" title="Read Modification Options">
            <param argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads for paired-end data, unless a separate value for the second read is specified. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
                <sanitizer>
                    <valid initial="string.digits"><add value="," /></valid>
                </sanitizer>
                <validator type="regex">[0-9,]+</validator>
            </param>

            <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option>
            <option value="too_short_file">Too short reads: write reads that are too short according to minimum length specified (default: discard reads).</option>
            <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option>
            <option value="untrimmed_file">Untrimmed reads: write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file (default: output to same file as trimmed)</option>
            <option value="multiple_output">Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)</option>
            <option value="json_stats">Statistics in JSON format</option>
        </param>
    </inputs>

    <outputs>
        <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">

        <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
            <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
            <filter>output_selector and 'too_long_file' in output_selector</filter>
            <expand macro="inherit_format_2" />
        </data>
        <data name="json_stats" format="json" from_work_dir="stats.json" label="${tool.name} on ${on_string}: Statistics (JSON)" >
            <filter>output_selector and 'json_stats' in output_selector</filter>
        </data>
        <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" format="fastqsanger" >
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
            <filter>output_selector and 'multiple_output' in output_selector</filter>
        </collection>
    </outputs>

            <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
            <assert_command>
                <has_text text="--discard-trimmed"/>
            </assert_command>
        </test>
        <!-- Ensure rest file output works, test json output -->
        <test expect_num_outputs="3">
            <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>

                    </conditional>
                </repeat>
            </section>
            <param name="output_filtering" value="default"/>
            <param name="read_modification" value="none"/>
            <param name="output_selector" value="rest_file,json_stats"/>
            <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
            <output name="json_stats" file="cutadapt_rest.json" ftype="json"/>
            <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
        </test>
        <!-- Ensure nextseq-trim option works -->
        <test expect_num_outputs="1">
            <param name="type" value="single" />

            <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
            <assert_command>
                <has_text text="TGTAGGCCX"/>
            </assert_command>
        </test>
        <!-- Ensure individual per adapter noindels parameter works -->
        <test expect_num_outputs="3">
            <param name="type" value="paired_collection" />
            <param name="input_1">
                <collection type="paired">
                    <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
                    <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
                </collection>
            </param>
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGATCGGAAGAGC"/>
                    </conditional>
                    <param name="single_noindels" value=";noindels" />
                </repeat>
            </section>
            <section name="r2">
                <repeat name="adapters2">
                    <conditional name="adapter_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                    <param name="single_noindels" value=";noindels" />
                </repeat>
            </section>
            <output_collection name="out_pairs" type="paired">
                <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
                <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
            </output_collection>
        </test>
        <!-- Ensure specifying quality cutoff (for both reads) works -->
        <test expect_num_outputs="3">
            <param name="type" value="paired_collection" />
            <param name="input_1">
                <collection type="paired">
                    <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
                    <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
                </collection>
            </param>
            <param name="quality_cutoff" value="5" />
            <section name="r1">
                <repeat name="adapters">
                    <conditional name="adapter_source">
                        <param name="adapter_source_list" value="user"/>
                        <param name="adapter" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
            </section>
            <section name="r2">
                <repeat name="adapters2">
                    <conditional name="adapter_source2">
                        <param name="adapter_source_list2" value="user"/>
                        <param name="adapter2" value="AGATCGGAAGAGC"/>
                    </conditional>
                </repeat>
                <param name="quality_cutoff2" value="15,20"/>
            </section>
            <output_collection name="out_pairs" type="paired">
                <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
                <element name="reverse" decompress="True" file="cutadapt_out2_cutoff.fq.gz" ftype="fastq.gz" />
            </output_collection>
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark