<commit_before><tool id="yac" name="Clip adapter" version="1.3.6">
    <description />
    <command interpreter="python">yac.py --input $input
                                       --output $output
                                       --output_format "$out_format"
                                       --adapter_to_clip $clip_source.clip_sequence
                                       --min $min
                                       --max $max
                                       --Nmode $Nmode
  </command>
    <inputs>
        <param format="fastq" label="Source file" name="input" type="data" />
        <param label="min size" name="min" size="4" type="integer" value="15" />
        <param label="max size" name="max" size="4" type="integer" value="36" />
        <param label="Select output format" name="out_format" type="select">
            <option selected="true" value="fasta">Fasta format</option>
            <option value="fastq">Fastq format</option>
        </param>
        <param label="Accept reads containing N?" name="Nmode" type="select">
            <option selected="True" value="accept">accept</option>
            <option value="reject">reject</option>
        </param>
        <conditional name="clip_source">
            <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select">
                <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option>
                <option value="user">Use custom sequence</option>
            </param>
            <when value="prebuilt">
                <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select">
                    <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
                    <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
                    <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq  TGGAATTCTCGGGTGCCAAG</option>
                    <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option>
                </param>
            </when>
            <when value="user">
                <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="fasta" metadata_source="input" name="output">
          <change_format>
              <when input="out_format" value="fastq" format="fastq" />
          </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param ftype="fastqsanger" name="input" value="yac.fastq" />
            <param name="min" value="18" />
            <param name="max" value="29" />
            <param name="clip_source_list" value="prebuilt" />
            <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
            <param name="Nmode" value="accept" />
            <output file="yac.out" name="output" />
        </test>
        <test>
            <param ftype="fastqsanger" name="input" value="yac.fastq" />
            <param name="min" value="18" />
            <param name="max" value="29" />
            <param name="clip_source_list" value="prebuilt" />
            <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
            <param name="Nmode" value="accept" />
            <param name="out_format" value="fastq" />
            <output file="yac_fastq.out" name="output" />
        </test>
    </tests><commit_msg>The output file label has been modified as requested in issue #7<commit_after><tool id="yac" name="Clip adapter" version="1.3.6">
    <description />
    <command interpreter="python">yac.py --input $input
                                       --output $output
                                       --output_format "$out_format"
                                       --adapter_to_clip $clip_source.clip_sequence
                                       --min $min
                                       --max $max
                                       --Nmode $Nmode
  </command>
    <inputs>
        <param format="fastq" label="Source file" name="input" type="data" />
        <param label="min size" name="min" size="4" type="integer" value="15" />
        <param label="max size" name="max" size="4" type="integer" value="36" />
        <param label="Select output format" name="out_format" type="select">
            <option selected="true" value="fasta">Fasta format</option>
            <option value="fastq">Fastq format</option>
        </param>
        <param label="Accept reads containing N?" name="Nmode" type="select">
            <option selected="True" value="accept">accept</option>
            <option value="reject">reject</option>
        </param>
        <conditional name="clip_source">
            <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select">
                <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option>
                <option value="user">Use custom sequence</option>
            </param>
            <when value="prebuilt">
                <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select">
                    <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
                    <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
                    <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq  TGGAATTCTCGGGTGCCAAG</option>
                    <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option>
                </param>
            </when>
            <when value="user">
                <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="fasta" metadata_source="input" name="output" label="Clipping of ${input.name}">
          <change_format>
              <when input="out_format" value="fastq" format="fastq" />
          </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param ftype="fastqsanger" name="input" value="yac.fastq" />
            <param name="min" value="18" />
            <param name="max" value="29" />
            <param name="clip_source_list" value="prebuilt" />
            <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
            <param name="Nmode" value="accept" />
            <output file="yac.out" name="output" />
        </test>
        <test>
            <param ftype="fastqsanger" name="input" value="yac.fastq" />
            <param name="min" value="18" />
            <param name="max" value="29" />
            <param name="clip_source_list" value="prebuilt" />
            <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
            <param name="Nmode" value="accept" />
            <param name="out_format" value="fastq" />
            <output file="yac_fastq.out" name="output" />
        </test>
    </tests>
{'fraction_non_alphanumeric': 0.13998082454458294, 'fraction_numerical': 0.005341734009039857, 'mean_word_length': 2.06035205364627, 'pattern_counts': {'":': 0, '<': 147, '<?xml version=': 0, '>': 147, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 12, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7429348', 'n_tokens_mistral': 2137, 'n_tokens_neox': 2016, 'n_words': 435}