<commit_before><tool id="stringtie" name="StringTie" version="1.3.3">
    <description>transcript assembly and quantification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
    <![CDATA[
        mkdir ./special_de_output/ &&
        #if str($guide.use_guide) == 'yes':
            ln -s '$guide.guide_gff' ./special_de_output/ &&
        #end if

        #if $input_bam.metadata.ftype == 'sam':
            samtools sort -@ \${GALAXY_SLOTS:-1} "$input_bam" | stringtie
        #else
            stringtie "$input_bam"
        #end if

        -o "$output_gtf"
        -p "\${GALAXY_SLOTS:-1}"
        #if str($guide.use_guide) == 'yes':
            -C '$coverage'
            -G '$guide.guide_gff'
            $guide.input_estimation
            #if $guide.special_outputs != 'no':
                -b ./special_de_output/
            #end if
        #end if
        #if str($option_set.options) == 'advanced':
            -l '$option_set.name_prefix'
            -f '$option_set.fraction'
            -m '$option_set.min_tlen'
            -a '$option_set.min_anchor_len'
            -j '$option_set.min_anchor_cov'
            -c '$option_set.min_bundle_cov'
            -g '$option_set.bdist'
            -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
            #if $option_set.abundance_estimation:
                -A "$gene_abundance_estimation"
            #end if
            #if str($option_set.omit_sequences).strip() != "":
                -x "$option_set.omit_sequences"
            #end if
        #end if

        #if str($guide.use_guide) == 'yes':
            #if $guide.special_outputs.special_outputs_select == 'deseq2':
                &&
                ls -l ./special_de_output/
                &&
                prepDE.py
                    -i ./special_de_output/<commit_msg>We only have one sample<commit_after><tool id="stringtie" name="StringTie" version="1.3.3">
    <description>transcript assembly and quantification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
    <![CDATA[
        mkdir -p ./special_de_output/sample1/ &&
        #if str($guide.use_guide) == 'yes':
            ln -s '$guide.guide_gff' ./special_de_output/sample1/ &&
        #end if

        #if $input_bam.metadata.ftype == 'sam':
            samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' | stringtie
        #else
            stringtie '$input_bam'
        #end if

        -o "$output_gtf"
        -p "\${GALAXY_SLOTS:-1}"
        #if str($guide.use_guide) == 'yes':
            -C '$coverage'
            -G '$guide.guide_gff'
            $guide.input_estimation
            #if $guide.special_outputs != 'no':
                -b ./special_de_output/sample1/
            #end if
        #end if
        #if str($option_set.options) == 'advanced':
            -l '$option_set.name_prefix'
            -f '$option_set.fraction'
            -m '$option_set.min_tlen'
            -a '$option_set.min_anchor_len'
            -j '$option_set.min_anchor_cov'
            -c '$option_set.min_bundle_cov'
            -g '$option_set.bdist'
            -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
            #if $option_set.abundance_estimation:
                -A "$gene_abundance_estimation"
            #end if
            #if str($option_set.omit_sequences).strip() != "":
                -x "$option_set.omit_sequences"
            #end if
        #end if

        #if str($guide.use_guide) == 'yes':
            #if $guide.special_outputs.special_outputs_select == 'deseq2':
                &&
                ls -l ./special_de_output/
                &&
                prepDE.py
                    -i ./special_de_output/
{'fraction_non_alphanumeric': 0.13550135501355012, 'fraction_numerical': 0.003695491500369549, 'mean_word_length': 1.7432432432432432, 'pattern_counts': {'":': 2, '<': 27, '<?xml version=': 0, '>': 25, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3804319', 'n_tokens_mistral': 1358, 'n_tokens_neox': 1267, 'n_words': 228}